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

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	+	#include <stack>
44		#include "selection/SelectionEvaluator.hpp"
45	<	namespace oopse {
45	>	#include "primitives/Atom.hpp"
46	>	#include "primitives/DirectionalAtom.hpp"
47	>	#include "primitives/RigidBody.hpp"
48	>	#include "primitives/Molecule.hpp"
49	>	#include "io/ifstrstream.hpp"
50	>	#include "types/FixedChargeAdapter.hpp"
51	>	#include "types/FluctuatingChargeAdapter.hpp"
52	>
53	>
54	>	namespace OpenMD {
55	>
56	>
57	>	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
58	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
59	>	indexFinder(info),
60	>	isLoaded_(false){
61	>	nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
62	>	}
63	>
64	>	bool SelectionEvaluator::loadScript(const std::string& filename,
65	>	const std::string& script) {
66	>	clearDefinitionsAndLoadPredefined();
67	>	this->filename = filename;
68	>	this->script = script;
69	>	if (! compiler.compile(filename, script)) {
70	>	error = true;
71	>	errorMessage = compiler.getErrorMessage();
72	>
73	>	sprintf( painCave.errMsg,
74	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
75	>	painCave.severity = OPENMD_ERROR;
76	>	painCave.isFatal = 1;
77	>	simError();
78	>	return false;
79	>	}
80	>
81	>	pc = 0;
82	>	aatoken = compiler.getAatokenCompiled();
83	>	linenumbers = compiler.getLineNumbers();
84	>	lineIndices = compiler.getLineIndices();
85	>
86	>	std::vector<std::vector<Token> >::const_iterator i;
87	>
88	>	isDynamic_ = false;
89	>	for (i = aatoken.begin(); i != aatoken.end(); ++i) {
90	>	if (containDynamicToken(*i)) {
91	>	isDynamic_ = true;
92	>	break;
93	>	}
94	>	}
95	>
96	>	isLoaded_ = true;
97	>	return true;
98	>	}
99	>
100	>	void SelectionEvaluator::clearState() {
101	>	error = false;
102	>	errorMessage = "";
103	>	}
104	>
105	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
106	>	clearState();
107	>	return loadScript("", script);
108	>	}
109	>
110	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
111	>	clearState();
112	>	return loadScriptFileInternal(filename);
113	>	}
114	>
115	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
116	>	ifstrstream ifs(filename.c_str());
117	>	if (!ifs.is_open()) {
118	>	return false;
119	>	}
120	>
121	>	const int bufferSize = 65535;
122	>	char buffer[bufferSize];
123	>	std::string script;
124	>	while(ifs.getline(buffer, bufferSize)) {
125	>	script += buffer;
126	>	}
127	>	return loadScript(filename, script);
128	>	}
129	>
130	>	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
131	>
132	>	while ( pc < aatoken.size()) {
133	>	statement = aatoken[pc++];
134	>	statementLength = statement.size();
135	>	Token token = statement[0];
136	>	switch (token.tok) {
137	>	case Token::define:
138	>	define();
139	>	break;
140	>	case Token::select:
141	>	select(bs);
142	>	break;
143	>	default:
144	>	unrecognizedCommand(token);
145	>	return;
146	>	}
147	>	}
148	>
149	>	}
150	>
151	>	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs, int frame){
152	>
153	>	while ( pc < aatoken.size()) {
154	>	statement = aatoken[pc++];
155	>	statementLength = statement.size();
156	>	Token token = statement[0];
157	>	switch (token.tok) {
158	>	case Token::define:
159	>	define();
160	>	break;
161	>	case Token::select:
162	>	select(bs, frame);
163	>	break;
164	>	default:
165	>	unrecognizedCommand(token);
166	>	return;
167	>	}
168	>	}
169	>
170	>	}
171	>
172	>	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
173	>	int pcStart) {
174	>	OpenMDBitSet bs;
175	>	std::stack<OpenMDBitSet> stack;
176	>
177	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
178	>	Token instruction = code[pc];
179	>
180	>	switch (instruction.tok) {
181	>	case Token::expressionBegin:
182	>	break;
183	>	case Token::expressionEnd:
184	>	break;
185	>	case Token::all:
186	>	bs = allInstruction();
187	>	stack.push(bs);
188	>	break;
189	>	case Token::none:
190	>	bs = OpenMDBitSet(nStuntDouble);
191	>	stack.push(bs);
192	>	break;
193	>	case Token::opOr:
194	>	bs = stack.top();
195	>	stack.pop();
196	>	stack.top() |= bs;
197	>	break;
198	>	case Token::opAnd:
199	>	bs = stack.top();
200	>	stack.pop();
201	>	stack.top() &= bs;
202	>	break;
203	>	case Token::opNot:
204	>	stack.top().flip();
205	>	break;
206	>	case Token::within:
207	>	withinInstruction(instruction, stack.top());
208	>	break;
209	>	case Token::hull:
210	>	stack.push(hull());
211	>	break;
212	>	//case Token::selected:
213	>	//  stack.push(getSelectionSet());
214	>	//  break;
215	>	case Token::name:
216	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
217	>	break;
218	>	case Token::index:
219	>	stack.push(indexInstruction(instruction.value));
220	>	break;
221	>	case Token::identifier:
222	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
223	>	break;
224	>	case Token::opLT:
225	>	case Token::opLE:
226	>	case Token::opGE:
227	>	case Token::opGT:
228	>	case Token::opEQ:
229	>	case Token::opNE:
230	>	stack.push(comparatorInstruction(instruction));
231	>	break;
232	>	default:
233	>	unrecognizedExpression();
234	>	}
235	>	}
236	>	if (stack.size() != 1)
237	>	evalError("atom expression compiler error - stack over/underflow");
238	>
239	>	return stack.top();
240	>	}
241	>
242	>
243	>	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
244	>	int pcStart, int frame) {
245	>	OpenMDBitSet bs;
246	>	std::stack<OpenMDBitSet> stack;
247	>
248	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
249	>	Token instruction = code[pc];
250	>
251	>	switch (instruction.tok) {
252	>	case Token::expressionBegin:
253	>	break;
254	>	case Token::expressionEnd:
255	>	break;
256	>	case Token::all:
257	>	bs = allInstruction();
258	>	stack.push(bs);
259	>	break;
260	>	case Token::none:
261	>	bs = OpenMDBitSet(nStuntDouble);
262	>	stack.push(bs);
263	>	break;
264	>	case Token::opOr:
265	>	bs = stack.top();
266	>	stack.pop();
267	>	stack.top() |= bs;
268	>	break;
269	>	case Token::opAnd:
270	>	bs = stack.top();
271	>	stack.pop();
272	>	stack.top() &= bs;
273	>	break;
274	>	case Token::opNot:
275	>	stack.top().flip();
276	>	break;
277	>	case Token::within:
278	>	withinInstruction(instruction, stack.top(), frame);
279	>	break;
280	>	case Token::hull:
281	>	stack.push(hull(frame));
282	>	break;
283	>	//case Token::selected:
284	>	//  stack.push(getSelectionSet());
285	>	//  break;
286	>	case Token::name:
287	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
288	>	break;
289	>	case Token::index:
290	>	stack.push(indexInstruction(instruction.value));
291	>	break;
292	>	case Token::identifier:
293	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
294	>	break;
295	>	case Token::opLT:
296	>	case Token::opLE:
297	>	case Token::opGE:
298	>	case Token::opGT:
299	>	case Token::opEQ:
300	>	case Token::opNE:
301	>	stack.push(comparatorInstruction(instruction, frame));
302	>	break;
303	>	default:
304	>	unrecognizedExpression();
305	>	}
306	>	}
307	>	if (stack.size() != 1)
308	>	evalError("atom expression compiler error - stack over/underflow");
309	>
310	>	return stack.top();
311	>	}
312	>
313	>
314	>
315	>	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
316	>	int comparator = instruction.tok;
317	>	int property = instruction.intValue;
318	>	float comparisonValue = boost::any_cast<float>(instruction.value);
319	>	OpenMDBitSet bs(nStuntDouble);
320	>	bs.clearAll();
321	>
322	>	SimInfo::MoleculeIterator mi;
323	>	Molecule* mol;
324	>	Molecule::AtomIterator ai;
325	>	Atom* atom;
326	>	Molecule::RigidBodyIterator rbIter;
327	>	RigidBody* rb;
328	>
329	>	for (mol = info->beginMolecule(mi); mol != NULL;
330	>	mol = info->nextMolecule(mi)) {
331	>
332	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
333	>	compareProperty(atom, bs, property, comparator, comparisonValue);
334	>	}
335	>
336	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
337	>	rb = mol->nextRigidBody(rbIter)) {
338	>	compareProperty(rb, bs, property, comparator, comparisonValue);
339	>	}
340	>	}
341	>
342	>	return bs;
343	>	}
344	>
345	>	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
346	>	int comparator = instruction.tok;
347	>	int property = instruction.intValue;
348	>	float comparisonValue = boost::any_cast<float>(instruction.value);
349	>	OpenMDBitSet bs(nStuntDouble);
350	>	bs.clearAll();
351	>
352	>	SimInfo::MoleculeIterator mi;
353	>	Molecule* mol;
354	>	Molecule::AtomIterator ai;
355	>	Atom* atom;
356	>	Molecule::RigidBodyIterator rbIter;
357	>	RigidBody* rb;
358	>
359	>	for (mol = info->beginMolecule(mi); mol != NULL;
360	>	mol = info->nextMolecule(mi)) {
361	>
362	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
363	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
364	>	}
365	>
366	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
367	>	rb = mol->nextRigidBody(rbIter)) {
368	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
369	>	}
370	>	}
371	>
372	>	return bs;
373	>	}
374	>
375	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
376	>	int property, int comparator,
377	>	float comparisonValue) {
378	>	RealType propertyValue = 0.0;
379	>	Vector3d pos;
380	>	switch (property) {
381	>	case Token::mass:
382	>	propertyValue = sd->getMass();
383	>	break;
384	>	case Token::charge:
385	>	if (sd->isAtom()){
386	>	Atom* atom = static_cast<Atom*>(sd);
387	>	propertyValue = getCharge(atom);
388	>	} else if (sd->isRigidBody()) {
389	>	RigidBody* rb = static_cast<RigidBody*>(sd);
390	>	RigidBody::AtomIterator ai;
391	>	Atom* atom;
392	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
393	>	propertyValue+=  getCharge(atom);
394	>	}
395	>	}
396	>	break;
397	>	case Token::x:
398	>	propertyValue = sd->getPos().x();
399	>	break;
400	>	case Token::y:
401	>	propertyValue = sd->getPos().y();
402	>	break;
403	>	case Token::z:
404	>	propertyValue = sd->getPos().z();
405	>	break;
406	>	case Token::wrappedX:
407	>	pos = sd->getPos();
408	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
409	>	propertyValue = pos.x();
410	>	break;
411	>	case Token::wrappedY:
412	>	pos = sd->getPos();
413	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
414	>	propertyValue = pos.y();
415	>	break;
416	>	case Token::wrappedZ:
417	>	pos = sd->getPos();
418	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
419	>	propertyValue = pos.z();
420	>	break;
421	>	case Token::r:
422	>	propertyValue = sd->getPos().length();
423	>	break;
424	>	default:
425	>	unrecognizedAtomProperty(property);
426	>	}
427	>
428	>	bool match = false;
429	>	switch (comparator) {
430	>	case Token::opLT:
431	>	match = propertyValue < comparisonValue;
432	>	break;
433	>	case Token::opLE:
434	>	match = propertyValue <= comparisonValue;
435	>	break;
436	>	case Token::opGE:
437	>	match = propertyValue >= comparisonValue;
438	>	break;
439	>	case Token::opGT:
440	>	match = propertyValue > comparisonValue;
441	>	break;
442	>	case Token::opEQ:
443	>	match = propertyValue == comparisonValue;
444	>	break;
445	>	case Token::opNE:
446	>	match = propertyValue != comparisonValue;
447	>	break;
448	>	}
449	>	if (match)
450	>	bs.setBitOn(sd->getGlobalIndex());
451
452	+
453	+	}
454
455	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
456	+	int property, int comparator,
457	+	float comparisonValue, int frame) {
458	+	RealType propertyValue = 0.0;
459	+	Vector3d pos;
460	+	switch (property) {
461	+	case Token::mass:
462	+	propertyValue = sd->getMass();
463	+	break;
464	+	case Token::charge:
465	+	if (sd->isAtom()){
466	+	Atom* atom = static_cast<Atom*>(sd);
467	+	propertyValue = getCharge(atom,frame);
468	+	} else if (sd->isRigidBody()) {
469	+	RigidBody* rb = static_cast<RigidBody*>(sd);
470	+	RigidBody::AtomIterator ai;
471	+	Atom* atom;
472	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
473	+	propertyValue+=  getCharge(atom,frame);
474	+	}
475	+	}
476	+	break;
477	+	case Token::x:
478	+	propertyValue = sd->getPos(frame).x();
479	+	break;
480	+	case Token::y:
481	+	propertyValue = sd->getPos(frame).y();
482	+	break;
483	+	case Token::z:
484	+	propertyValue = sd->getPos(frame).z();
485	+	break;
486	+	case Token::wrappedX:
487	+	pos = sd->getPos(frame);
488	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
489	+	propertyValue = pos.x();
490	+	break;
491	+	case Token::wrappedY:
492	+	pos = sd->getPos(frame);
493	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
494	+	propertyValue = pos.y();
495	+	break;
496	+	case Token::wrappedZ:
497	+	pos = sd->getPos(frame);
498	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
499	+	propertyValue = pos.z();
500	+	break;
501	+
502	+	case Token::r:
503	+	propertyValue = sd->getPos(frame).length();
504	+	break;
505	+	default:
506	+	unrecognizedAtomProperty(property);
507	+	}
508	+
509	+	bool match = false;
510	+	switch (comparator) {
511	+	case Token::opLT:
512	+	match = propertyValue < comparisonValue;
513	+	break;
514	+	case Token::opLE:
515	+	match = propertyValue <= comparisonValue;
516	+	break;
517	+	case Token::opGE:
518	+	match = propertyValue >= comparisonValue;
519	+	break;
520	+	case Token::opGT:
521	+	match = propertyValue > comparisonValue;
522	+	break;
523	+	case Token::opEQ:
524	+	match = propertyValue == comparisonValue;
525	+	break;
526	+	case Token::opNE:
527	+	match = propertyValue != comparisonValue;
528	+	break;
529	+	}
530	+	if (match)
531	+	bs.setBitOn(sd->getGlobalIndex());
532	+
533	+
534	+	}
535	+
536	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
537	+	OpenMDBitSet& bs){
538	+
539	+	boost::any withinSpec = instruction.value;
540	+	float distance;
541	+	if (withinSpec.type() == typeid(float)){
542	+	distance = boost::any_cast<float>(withinSpec);
543	+	} else if (withinSpec.type() == typeid(int)) {
544	+	distance = boost::any_cast<int>(withinSpec);
545	+	} else {
546	+	evalError("casting error in withinInstruction");
547	+	bs.clearAll();
548	+	}
549	+
550	+	bs = distanceFinder.find(bs, distance);
551	+	}
552	+
553	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
554	+	OpenMDBitSet& bs, int frame){
555	+
556	+	boost::any withinSpec = instruction.value;
557	+	float distance;
558	+	if (withinSpec.type() == typeid(float)){
559	+	distance = boost::any_cast<float>(withinSpec);
560	+	} else if (withinSpec.type() == typeid(int)) {
561	+	distance = boost::any_cast<int>(withinSpec);
562	+	} else {
563	+	evalError("casting error in withinInstruction");
564	+	bs.clearAll();
565	+	}
566	+
567	+	bs = distanceFinder.find(bs, distance, frame);
568	+	}
569	+
570	+	void SelectionEvaluator::define() {
571	+	assert(statement.size() >= 3);
572	+
573	+	std::string variable = boost::any_cast<std::string>(statement[1].value);
574	+
575	+	variables.insert(VariablesType::value_type(variable,
576	+	expression(statement, 2)));
577	+	}
578	+
579	+
580	+	/** @todo */
581	+	void SelectionEvaluator::predefine(const std::string& script) {
582	+
583	+	if (compiler.compile("#predefine", script)) {
584	+	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
585	+	if (aatoken.size() != 1) {
586	+	evalError("predefinition does not have exactly 1 command:"
587	+	+ script);
588	+	return;
589	+	}
590	+	std::vector<Token> statement = aatoken[0];
591	+	if (statement.size() > 2) {
592	+	int tok = statement[1].tok;
593	+	if (tok == Token::identifier ||
594	+	(tok & Token::predefinedset) == Token::predefinedset) {
595	+	std::string variable = boost::any_cast<std::string>(statement[1].value);
596	+	variables.insert(VariablesType::value_type(variable, statement));
597	+
598	+	} else {
599	+	evalError("invalid variable name:" + script);
600	+	}
601	+	}else {
602	+	evalError("bad predefinition length:" + script);
603	+	}
604	+
605	+	} else {
606	+	evalError("predefined set compile error:" + script +
607	+	"\ncompile error:" + compiler.getErrorMessage());
608	+	}
609	+	}
610	+
611	+	void SelectionEvaluator::select(OpenMDBitSet& bs){
612	+	bs = expression(statement, 1);
613	+	}
614	+
615	+	void SelectionEvaluator::select(OpenMDBitSet& bs, int frame){
616	+	bs = expression(statement, 1, frame);
617	+	}
618	+
619	+	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
620	+
621	+	OpenMDBitSet bs(nStuntDouble);
622	+	std::map<std::string, boost::any>::iterator i = variables.find(variable);
623	+
624	+	if (i != variables.end()) {
625	+	if (i->second.type() == typeid(OpenMDBitSet)) {
626	+	return boost::any_cast<OpenMDBitSet>(i->second);
627	+	} else if (i->second.type() ==  typeid(std::vector<Token>)){
628	+	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
629	+	i->second =  bs; /**@todo fixme */
630	+	return bs;
631	+	}
632	+	} else {
633	+	unrecognizedIdentifier(variable);
634	+	}
635	+
636	+	return bs;
637	+	}
638	+
639	+	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
640	+	return nameFinder.match(name);
641	+	}
642	+
643	+	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
644	+	std::vector<Token>::const_iterator i;
645	+	for (i = tokens.begin(); i != tokens.end(); ++i) {
646	+	if (i->tok & Token::dynamic) {
647	+	return true;
648	+	}
649	+	}
650	+
651	+	return false;
652	+	}
653	+
654	+	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
655	+	variables.clear();
656	+	//load predefine
657	+	//predefine();
658	+	}
659	+
660	+	OpenMDBitSet SelectionEvaluator::evaluate() {
661	+	OpenMDBitSet bs(nStuntDouble);
662	+	if (isLoaded_) {
663	+	pc = 0;
664	+	instructionDispatchLoop(bs);
665	+	}
666	+	return bs;
667	+	}
668	+
669	+	OpenMDBitSet SelectionEvaluator::evaluate(int frame) {
670	+	OpenMDBitSet bs(nStuntDouble);
671	+	if (isLoaded_) {
672	+	pc = 0;
673	+	instructionDispatchLoop(bs, frame);
674	+	}
675	+	return bs;
676	+	}
677	+
678	+	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
679	+	OpenMDBitSet bs(nStuntDouble);
680	+
681	+	if (value.type() == typeid(int)) {
682	+	int index = boost::any_cast<int>(value);
683	+	if (index < 0 || index >= bs.size()) {
684	+	invalidIndex(index);
685	+	} else {
686	+	bs = indexFinder.find(index);
687	+	}
688	+	} else if (value.type() == typeid(std::pair<int, int>)) {
689	+	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
690	+	assert(indexRange.first <= indexRange.second);
691	+	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
692	+	invalidIndexRange(indexRange);
693	+	}else {
694	+	bs = indexFinder.find(indexRange.first, indexRange.second);
695	+	}
696	+	}
697	+
698	+	return bs;
699	+	}
700	+
701	+	OpenMDBitSet SelectionEvaluator::allInstruction() {
702	+	OpenMDBitSet bs(nStuntDouble);
703	+
704	+	SimInfo::MoleculeIterator mi;
705	+	Molecule* mol;
706	+	Molecule::AtomIterator ai;
707	+	Atom* atom;
708	+	Molecule::RigidBodyIterator rbIter;
709	+	RigidBody* rb;
710	+
711	+	// Doing the loop insures that we're actually on this processor.
712	+
713	+	for (mol = info->beginMolecule(mi); mol != NULL;
714	+	mol = info->nextMolecule(mi)) {
715	+
716	+	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
717	+	bs.setBitOn(atom->getGlobalIndex());
718	+	}
719	+
720	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
721	+	rb = mol->nextRigidBody(rbIter)) {
722	+	bs.setBitOn(rb->getGlobalIndex());
723	+	}
724	+	}
725	+
726	+	return bs;
727	+	}
728	+
729	+	OpenMDBitSet SelectionEvaluator::hull() {
730	+	OpenMDBitSet bs(nStuntDouble);
731	+
732	+	bs = hullFinder.findHull();
733	+
734	+	return bs;
735	+	}
736	+
737	+
738	+	OpenMDBitSet SelectionEvaluator::hull(int frame) {
739	+	OpenMDBitSet bs(nStuntDouble);
740	+
741	+	bs = hullFinder.findHull(frame);
742	+
743	+	return bs;
744	+	}
745	+
746	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
747	+	RealType charge = 0.0;
748	+	AtomType* atomType = atom->getAtomType();
749	+
750	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
751	+	if ( fca.isFixedCharge() ) {
752	+	charge = fca.getCharge();
753	+	}
754	+
755	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
756	+	if ( fqa.isFluctuatingCharge() ) {
757	+	charge += atom->getFlucQPos();
758	+	}
759	+	return charge;
760	+	}
761	+
762	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
763	+	RealType charge = 0.0;
764	+	AtomType* atomType = atom->getAtomType();
765	+
766	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
767	+	if ( fca.isFixedCharge() ) {
768	+	charge = fca.getCharge();
769	+	}
770	+
771	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
772	+	if ( fqa.isFluctuatingCharge() ) {
773	+	charge += atom->getFlucQPos(frame);
774	+	}
775	+	return charge;
776	+	}
777	+
778		}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

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