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

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 283 by tim, Thu Feb 3 23:14:05 2005 UTC vs.
Revision 1931 by gezelter, Mon Aug 19 19:20:32 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>
#	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	+	#include "types/FixedChargeAdapter.hpp"
51	+	#include "types/FluctuatingChargeAdapter.hpp"
52
49	–	namespace oopse {
53
54	+	namespace OpenMD {
55
52	–	SelectionEvaluator::SelectionEvaluator(SimInfo* si, const std::string& script) : info(si), finder(info){
53	–	}
56
57	<	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
57	>	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
58	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
59	>	indexFinder(info), hasSurfaceArea_(false),
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	<	return false;
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	<	}
98	>	}
99
100	<	void SelectionEvaluator::clearState() {
72	<	for (int i = scriptLevelMax; --i >= 0; )
73	<	stack[i].clear();
74	<	scriptLevel = 0;
100	>	void SelectionEvaluator::clearState() {
101		error = false;
102		errorMessage = "";
103	<	}
103	>	}
104
105	<	bool SelectionEvaluator::loadScriptString(const std::string& script) {
105	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
106		clearState();
107		return loadScript("", script);
108	<	}
108	>	}
109
110	<	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
110	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
111		clearState();
112		return loadScriptFileInternal(filename);
113	<	}
113	>	}
114
115	<	bool SelectionEvaluator::loadScriptFileInternal(const  std::string & filename) {
116	<	return true; /**@todo */
117	<	}
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	<	void SelectionEvaluator::instructionDispatchLoop(){
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();
163	<	break;
164	<	default:
165	<	unrecognizedCommand(token);
166	<	return;
167	<	}
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		}
111	–	}
169
170	<	BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
171	<	BitSet bs;
172	<	std::stack<BitSet> stack;
173	<
174	<	for (int pc = pcStart; ; ++pc) {
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) {
#	Line 123 | Line 183 | void SelectionEvaluator::instructionDispatchLoop(){
183		case Token::expressionEnd:
184		break;
185		case Token::all:
186	<	bs = BitSet(nStuntDouble);
127	<	bs.setAll();
186	>	bs = allInstruction();
187		stack.push(bs);
188		break;
189		case Token::none:
190	<	bs = BitSet(nStuntDouble);
190	>	bs = OpenMDBitSet(nStuntDouble);
191		stack.push(bs);
192		break;
193		case Token::opOr:
#	Line 145 | Line 204 | void SelectionEvaluator::instructionDispatchLoop(){
204		stack.top().flip();
205		break;
206		case Token::within:
148	–
207		withinInstruction(instruction, stack.top());
208		break;
209	<	//case Token::selected:
210	<	//  stack.push(getSelectionSet());
211	<	//  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)));
#	Line 177 | Line 240 | void SelectionEvaluator::instructionDispatchLoop(){
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	<	BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
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	<	float propertyValue;
320	<	BitSet bs(nStuntDouble);
319	>	OpenMDBitSet bs(nStuntDouble);
320	>	bs.clearAll();
321
322		SimInfo::MoleculeIterator mi;
323		Molecule* mol;
#	Line 191 | Line 325 | BitSet SelectionEvaluator::comparatorInstruction(const
325		Atom* atom;
326		Molecule::RigidBodyIterator rbIter;
327		RigidBody* rb;
194	–
195	–	for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
328
329	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
330	<	compareProperty(atom, bs, property, comparator, comparisonValue);
331	<	}
332	<
333	<	//change the positions of atoms which belong to the rigidbodies
334	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
335	<	compareProperty(rb, bs, property, comparator, comparisonValue);
336	<	}
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	<	}
343	>	}
344
345	<	void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
346	<	double propertyValue;
347	<	switch (property) {
348	<	case Token::mass:
349	<	propertyValue = sd->getMass();
350	<	break;
216	<	case Token::charge:
217	<	return;
218	<	//break;
219	<	case Token::dipole:
220	<	return;
221	<	//break;
222	<	default:
223	<	unrecognizedAtomProperty(property);
224	<	}
225	<
226	<	bool match = false;
227	<	switch (comparator) {
228	<	case Token::opLT:
229	<	match = propertyValue < comparisonValue;
230	<	break;
231	<	case Token::opLE:
232	<	match = propertyValue <= comparisonValue;
233	<	break;
234	<	case Token::opGE:
235	<	match = propertyValue >= comparisonValue;
236	<	break;
237	<	case Token::opGT:
238	<	match = propertyValue > comparisonValue;
239	<	break;
240	<	case Token::opEQ:
241	<	match = propertyValue == comparisonValue;
242	<	break;
243	<	case Token::opNE:
244	<	match = propertyValue != comparisonValue;
245	<	break;
246	<	}
247	<	if (match)
248	<	bs.setBitOn(sd->getGlobalIndex());
249	<
250	<	}
251	<
252	<	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
253	<
254	<	boost::any withinSpec = instruction.value;
255	<	if (withinSpec.type() == typeid(float)){
256	<	//
257	<	return;
258	<	}
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	<	evalError("Unrecognized within parameter");
353	<	}
352	>	SimInfo::MoleculeIterator mi;
353	>	Molecule* mol;
354	>	Molecule::AtomIterator ai;
355	>	Atom* atom;
356	>	Molecule::RigidBodyIterator rbIter;
357	>	RigidBody* rb;
358
359	<	void SelectionEvaluator::define() {
360	<	assert(statement.size() >= 3);
359	>	for (mol = info->beginMolecule(mi); mol != NULL;
360	>	mol = info->nextMolecule(mi)) {
361
362	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
363	<
364	<	variables.insert(std::make_pair(variable, expression(statement, 2)));
365	<	}
366	<
367	<
368	<	/** @todo */
369	<	void SelectionEvaluator::predefine(const std::string& script) {
274	<
275	<	if (compiler.compile("#predefine", script)) {
276	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
277	<	if (aatoken.size() != 1) {
278	<	evalError("predefinition does not have exactly 1 command:"
279	<	+ script);
280	<	return;
281	<	}
282	<	std::vector<Token> statement = aatoken[0];
283	<	if (statement.size() > 2) {
284	<	int tok = statement[1].tok;
285	<	if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
286	<	std::string variable = boost::any_cast<std::string>(statement[1].value);
287	<	variables.insert(std::make_pair(variable, statement));
288	<
289	<	} else {
290	<	evalError("invalid variable name:" + script);
291	<	}
292	<	}else {
293	<	evalError("bad predefinition length:" + script);
294	<	}
295	<
296	<
297	<	} else {
298	<	evalError("predefined set compile error:" + script +
299	<	"\ncompile error:" + compiler.getErrorMessage());
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	<	}
372	>	return bs;
373	>	}
374
375	<	void SelectionEvaluator::select(){
376	<	//viewer.setSelectionSet(expression(statement, 1));
377	<	}
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
381	<	BitSet SelectionEvaluator::lookupValue(const std::string& variable){
381	>	switch (property) {
382	>	case Token::mass:
383	>	propertyValue = sd->getMass();
384	>	break;
385	>	case Token::charge:
386	>	if (sd->isAtom()){
387	>	Atom* atom = static_cast<Atom*>(sd);
388	>	propertyValue = getCharge(atom);
389	>	} else if (sd->isRigidBody()) {
390	>	RigidBody* rb = static_cast<RigidBody*>(sd);
391	>	RigidBody::AtomIterator ai;
392	>	Atom* atom;
393	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
394	>	propertyValue+=  getCharge(atom);
395	>	}
396	>	}
397	>	break;
398	>	case Token::x:
399	>	propertyValue = sd->getPos().x();
400	>	break;
401	>	case Token::y:
402	>	propertyValue = sd->getPos().y();
403	>	break;
404	>	case Token::z:
405	>	propertyValue = sd->getPos().z();
406	>	break;
407	>	case Token::wrappedX:
408	>	pos = sd->getPos();
409	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
410	>	propertyValue = pos.x();
411	>	break;
412	>	case Token::wrappedY:
413	>	pos = sd->getPos();
414	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
415	>	propertyValue = pos.y();
416	>	break;
417	>	case Token::wrappedZ:
418	>	pos = sd->getPos();
419	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
420	>	propertyValue = pos.z();
421	>	break;
422	>	case Token::r:
423	>	propertyValue = sd->getPos().length();
424	>	break;
425	>	default:
426	>	unrecognizedAtomProperty(property);
427	>	}
428	>
429	>	bool match = false;
430	>	switch (comparator) {
431	>	case Token::opLT:
432	>	match = propertyValue < comparisonValue;
433	>	break;
434	>	case Token::opLE:
435	>	match = propertyValue <= comparisonValue;
436	>	break;
437	>	case Token::opGE:
438	>	match = propertyValue >= comparisonValue;
439	>	break;
440	>	case Token::opGT:
441	>	match = propertyValue > comparisonValue;
442	>	break;
443	>	case Token::opEQ:
444	>	match = propertyValue == comparisonValue;
445	>	break;
446	>	case Token::opNE:
447	>	match = propertyValue != comparisonValue;
448	>	break;
449	>	}
450
451	<	std::map<std::string, boost::any>::iterator i = variables.find(variable);
451	>	if (match)
452	>	bs.setBitOn(sd->getGlobalIndex());
453
454	+
455	+	}
456	+
457	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
458	+	int property, int comparator,
459	+	float comparisonValue, int frame) {
460	+	RealType propertyValue = 0.0;
461	+	Vector3d pos;
462	+	switch (property) {
463	+	case Token::mass:
464	+	propertyValue = sd->getMass();
465	+	break;
466	+	case Token::charge:
467	+	if (sd->isAtom()){
468	+	Atom* atom = static_cast<Atom*>(sd);
469	+	propertyValue = getCharge(atom,frame);
470	+	} else if (sd->isRigidBody()) {
471	+	RigidBody* rb = static_cast<RigidBody*>(sd);
472	+	RigidBody::AtomIterator ai;
473	+	Atom* atom;
474	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
475	+	propertyValue+=  getCharge(atom,frame);
476	+	}
477	+	}
478	+	break;
479	+	case Token::x:
480	+	propertyValue = sd->getPos(frame).x();
481	+	break;
482	+	case Token::y:
483	+	propertyValue = sd->getPos(frame).y();
484	+	break;
485	+	case Token::z:
486	+	propertyValue = sd->getPos(frame).z();
487	+	break;
488	+	case Token::wrappedX:
489	+	pos = sd->getPos(frame);
490	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
491	+	propertyValue = pos.x();
492	+	break;
493	+	case Token::wrappedY:
494	+	pos = sd->getPos(frame);
495	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
496	+	propertyValue = pos.y();
497	+	break;
498	+	case Token::wrappedZ:
499	+	pos = sd->getPos(frame);
500	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
501	+	propertyValue = pos.z();
502	+	break;
503	+
504	+	case Token::r:
505	+	propertyValue = sd->getPos(frame).length();
506	+	break;
507	+	default:
508	+	unrecognizedAtomProperty(property);
509	+	}
510	+
511	+	bool match = false;
512	+	switch (comparator) {
513	+	case Token::opLT:
514	+	match = propertyValue < comparisonValue;
515	+	break;
516	+	case Token::opLE:
517	+	match = propertyValue <= comparisonValue;
518	+	break;
519	+	case Token::opGE:
520	+	match = propertyValue >= comparisonValue;
521	+	break;
522	+	case Token::opGT:
523	+	match = propertyValue > comparisonValue;
524	+	break;
525	+	case Token::opEQ:
526	+	match = propertyValue == comparisonValue;
527	+	break;
528	+	case Token::opNE:
529	+	match = propertyValue != comparisonValue;
530	+	break;
531	+	}
532	+	if (match)
533	+	bs.setBitOn(sd->getGlobalIndex());
534	+
535	+
536	+	}
537	+
538	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
539	+	OpenMDBitSet& bs){
540	+
541	+	boost::any withinSpec = instruction.value;
542	+	float distance;
543	+	if (withinSpec.type() == typeid(float)){
544	+	distance = boost::any_cast<float>(withinSpec);
545	+	} else if (withinSpec.type() == typeid(int)) {
546	+	distance = boost::any_cast<int>(withinSpec);
547	+	} else {
548	+	evalError("casting error in withinInstruction");
549	+	bs.clearAll();
550	+	}
551	+
552	+	bs = distanceFinder.find(bs, distance);
553	+	}
554	+
555	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
556	+	OpenMDBitSet& bs, int frame){
557	+
558	+	boost::any withinSpec = instruction.value;
559	+	float distance;
560	+	if (withinSpec.type() == typeid(float)){
561	+	distance = boost::any_cast<float>(withinSpec);
562	+	} else if (withinSpec.type() == typeid(int)) {
563	+	distance = boost::any_cast<int>(withinSpec);
564	+	} else {
565	+	evalError("casting error in withinInstruction");
566	+	bs.clearAll();
567	+	}
568	+
569	+	bs = distanceFinder.find(bs, distance, frame);
570	+	}
571	+
572	+	void SelectionEvaluator::define() {
573	+	assert(statement.size() >= 3);
574	+
575	+	std::string variable = boost::any_cast<std::string>(statement[1].value);
576	+
577	+	variables.insert(VariablesType::value_type(variable,
578	+	expression(statement, 2)));
579	+	}
580	+
581	+
582	+	/** @todo */
583	+	void SelectionEvaluator::predefine(const std::string& script) {
584	+
585	+	if (compiler.compile("#predefine", script)) {
586	+	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
587	+	if (aatoken.size() != 1) {
588	+	evalError("predefinition does not have exactly 1 command:"
589	+	+ script);
590	+	return;
591	+	}
592	+	std::vector<Token> statement = aatoken[0];
593	+	if (statement.size() > 2) {
594	+	int tok = statement[1].tok;
595	+	if (tok == Token::identifier ||
596	+	(tok & Token::predefinedset) == Token::predefinedset) {
597	+	std::string variable = boost::any_cast<std::string>(statement[1].value);
598	+	variables.insert(VariablesType::value_type(variable, statement));
599	+
600	+	} else {
601	+	evalError("invalid variable name:" + script);
602	+	}
603	+	}else {
604	+	evalError("bad predefinition length:" + script);
605	+	}
606	+
607	+	} else {
608	+	evalError("predefined set compile error:" + script +
609	+	"\ncompile error:" + compiler.getErrorMessage());
610	+	}
611	+	}
612	+
613	+	void SelectionEvaluator::select(OpenMDBitSet& bs){
614	+	bs = expression(statement, 1);
615	+	}
616	+
617	+	void SelectionEvaluator::select(OpenMDBitSet& bs, int frame){
618	+	bs = expression(statement, 1, frame);
619	+	}
620	+
621	+	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
622	+
623	+	OpenMDBitSet bs(nStuntDouble);
624	+	std::map<std::string, boost::any>::iterator i = variables.find(variable);
625	+
626		if (i != variables.end()) {
627	<	if (i->second.type() == typeid(BitSet)) {
628	<	return boost::any_cast<BitSet>(i->second);
629	<	} else if (i->second.type() ==  typeid(std::vector<Token>)){
630	<	BitSet bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
631	<	i->second =  bs; /**@todo fixme */
632	<	return bs;
633	<	}
627	>	if (i->second.type() == typeid(OpenMDBitSet)) {
628	>	return boost::any_cast<OpenMDBitSet>(i->second);
629	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
630	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
631	>	i->second =  bs; /**@todo fixme */
632	>	return bs;
633	>	}
634		} else {
635	<	unrecognizedIdentifier(variable);
635	>	unrecognizedIdentifier(variable);
636		}
637	<	}
637	>
638	>	return bs;
639	>	}
640	>
641	>	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
642	>	return nameFinder.match(name);
643	>	}
644
645	<	BitSet SelectionEvaluator::nameInstruction(const std::string& name){
646	<	BitSet bs(nStuntDouble);
645	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
646	>	std::vector<Token>::const_iterator i;
647	>	for (i = tokens.begin(); i != tokens.end(); ++i) {
648	>	if (i->tok & Token::dynamic) {
649	>	return true;
650	>	}
651	>	}
652
653	<	bool hasError = finder.match(name, bs);
653	>	return false;
654	>	}
655	>
656	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
657	>	variables.clear();
658	>	//load predefine
659	>	//predefine();
660	>	}
661	>
662	>	OpenMDBitSet SelectionEvaluator::evaluate() {
663	>	OpenMDBitSet bs(nStuntDouble);
664	>	if (isLoaded_) {
665	>	pc = 0;
666	>	instructionDispatchLoop(bs);
667	>	}
668	>	return bs;
669	>	}
670	>
671	>	OpenMDBitSet SelectionEvaluator::evaluate(int frame) {
672	>	OpenMDBitSet bs(nStuntDouble);
673	>	if (isLoaded_) {
674	>	pc = 0;
675	>	instructionDispatchLoop(bs, frame);
676	>	}
677	>	return bs;
678	>	}
679	>
680	>	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
681	>	OpenMDBitSet bs(nStuntDouble);
682	>
683	>	if (value.type() == typeid(int)) {
684	>	int index = boost::any_cast<int>(value);
685	>	if (index < 0 || index >= bs.size()) {
686	>	invalidIndex(index);
687	>	} else {
688	>	bs = indexFinder.find(index);
689	>	}
690	>	} else if (value.type() == typeid(std::pair<int, int>)) {
691	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
692	>	assert(indexRange.first <= indexRange.second);
693	>	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
694	>	invalidIndexRange(indexRange);
695	>	}else {
696	>	bs = indexFinder.find(indexRange.first, indexRange.second);
697	>	}
698	>	}
699	>
700	>	return bs;
701	>	}
702	>
703	>	OpenMDBitSet SelectionEvaluator::allInstruction() {
704	>	OpenMDBitSet bs(nStuntDouble);
705	>
706	>	SimInfo::MoleculeIterator mi;
707	>	Molecule* mol;
708	>	Molecule::AtomIterator ai;
709	>	Atom* atom;
710	>	Molecule::RigidBodyIterator rbIter;
711	>	RigidBody* rb;
712	>
713	>	// Doing the loop insures that we're actually on this processor.
714	>
715	>	for (mol = info->beginMolecule(mi); mol != NULL;
716	>	mol = info->nextMolecule(mi)) {
717	>
718	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
719	>	bs.setBitOn(atom->getGlobalIndex());
720	>	}
721	>
722	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
723	>	rb = mol->nextRigidBody(rbIter)) {
724	>	bs.setBitOn(rb->getGlobalIndex());
725	>	}
726	>	}
727	>
728	>	return bs;
729	>	}
730	>
731	>	OpenMDBitSet SelectionEvaluator::hull() {
732	>	OpenMDBitSet bs(nStuntDouble);
733
734	<	return bs;
735	<	}
734	>	bs = hullFinder.findHull();
735	>	surfaceArea_ = hullFinder.getSurfaceArea();
736	>	hasSurfaceArea_ = true;
737	>	return bs;
738	>	}
739
740
741	+	OpenMDBitSet SelectionEvaluator::hull(int frame) {
742	+	OpenMDBitSet bs(nStuntDouble);
743	+
744	+	bs = hullFinder.findHull(frame);
745	+
746	+	return bs;
747	+	}
748	+
749	+	RealType SelectionEvaluator::getCharge(Atom* atom) {
750	+	RealType charge = 0.0;
751	+	AtomType* atomType = atom->getAtomType();
752	+
753	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
754	+	if ( fca.isFixedCharge() ) {
755	+	charge = fca.getCharge();
756	+	}
757	+
758	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
759	+	if ( fqa.isFluctuatingCharge() ) {
760	+	charge += atom->getFlucQPos();
761	+	}
762	+	return charge;
763	+	}
764	+
765	+	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
766	+	RealType charge = 0.0;
767	+	AtomType* atomType = atom->getAtomType();
768	+
769	+	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
770	+	if ( fca.isFixedCharge() ) {
771	+	charge = fca.getCharge();
772	+	}
773	+
774	+	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
775	+	if ( fqa.isFluctuatingCharge() ) {
776	+	charge += atom->getFlucQPos(frame);
777	+	}
778	+	return charge;
779	+	}
780	+
781		}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 283 by tim, Thu Feb 3 23:14:05 2005 UTC vs.
Revision 1931 by gezelter, Mon Aug 19 19:20:32 2013 UTC

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