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

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 281 by tim, Wed Feb 2 23:13:11 2005 UTC vs.
Revision 2055 by gezelter, Fri Feb 6 18:49:27 2015 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	+	#include <stack>
44		#include "selection/SelectionEvaluator.hpp"
45	<	namespace oopse {
45	>	#include "primitives/Atom.hpp"
46	>	#include "primitives/DirectionalAtom.hpp"
47	>	#include "primitives/RigidBody.hpp"
48	>	#include "primitives/Molecule.hpp"
49	>	#include "io/ifstrstream.hpp"
50	>	#include "types/FixedChargeAdapter.hpp"
51	>	#include "types/FluctuatingChargeAdapter.hpp"
52
53
54	<	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
54	>	namespace OpenMD {
55	>
56	>
57	>	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
58	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
59	>	indexFinder(info), hasSurfaceArea_(false),
60	>	isLoaded_(false){
61	>	nObjects.push_back(info->getNGlobalAtoms() + info->getNGlobalRigidBodies());
62	>	nObjects.push_back(info->getNGlobalBonds());
63	>	nObjects.push_back(info->getNGlobalBends());
64	>	nObjects.push_back(info->getNGlobalTorsions());
65	>	nObjects.push_back(info->getNGlobalInversions());
66	>	nObjects.push_back(info->getNGlobalMolecules());
67	>	}
68	>
69	>	bool SelectionEvaluator::loadScript(const std::string& filename,
70	>	const std::string& script) {
71	>	clearDefinitionsAndLoadPredefined();
72		this->filename = filename;
73		this->script = script;
74		if (! compiler.compile(filename, script)) {
75	<	error = true;
76	<	errorMessage = compiler.getErrorMessage();
77	<	return false;
75	>	error = true;
76	>	errorMessage = compiler.getErrorMessage();
77	>
78	>	sprintf( painCave.errMsg,
79	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
80	>	painCave.severity = OPENMD_ERROR;
81	>	painCave.isFatal = 1;
82	>	simError();
83	>	return false;
84		}
85
86		pc = 0;
87		aatoken = compiler.getAatokenCompiled();
88		linenumbers = compiler.getLineNumbers();
89		lineIndices = compiler.getLineIndices();
90	+
91	+	std::vector<std::vector<Token> >::const_iterator i;
92	+
93	+	isDynamic_ = false;
94	+	for (i = aatoken.begin(); i != aatoken.end(); ++i) {
95	+	if (containDynamicToken(*i)) {
96	+	isDynamic_ = true;
97	+	break;
98	+	}
99	+	}
100	+
101	+	isLoaded_ = true;
102		return true;
103	<	}
103	>	}
104
105	<	void SelectionEvaluator::clearState() {
63	<	for (int i = scriptLevelMax; --i >= 0; )
64	<	stack[i].clear();
65	<	scriptLevel = 0;
105	>	void SelectionEvaluator::clearState() {
106		error = false;
107		errorMessage = "";
108	<	}
108	>	}
109
110	<	bool SelectionEvaluator::loadScriptString(const std::string& script) {
110	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
111		clearState();
112		return loadScript("", script);
113	<	}
113	>	}
114
115	<	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
115	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
116		clearState();
117		return loadScriptFileInternal(filename);
118	<	}
118	>	}
119
120	<
121	<	void SelectionEvaluator::instructionDispatchLoop(){
122	<
120	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
121	>	ifstrstream ifs(filename.c_str());
122	>	if (!ifs.is_open()) {
123	>	return false;
124	>	}
125	>
126	>	const int bufferSize = 65535;
127	>	char buffer[bufferSize];
128	>	std::string script;
129	>	while(ifs.getline(buffer, bufferSize)) {
130	>	script += buffer;
131	>	}
132	>	return loadScript(filename, script);
133	>	}
134	>
135	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){
136	>
137		while ( pc < aatoken.size()) {
138	<	statement = aatoken[pc++];
139	<	statementLength = statement.size();
140	<	Token token = statement[0];
141	<	switch (token.tok) {
142	<	case Token::define:
143	<	define();
144	<	break;
145	<	case Token::select:
146	<	select();
147	<	break;
148	<	default:
149	<	unrecognizedCommand(token);
150	<	return;
151	<	}
138	>	statement = aatoken[pc++];
139	>	statementLength = statement.size();
140	>	Token token = statement[0];
141	>	switch (token.tok) {
142	>	case Token::define:
143	>	define();
144	>	break;
145	>	case Token::select:
146	>	select(bs);
147	>	break;
148	>	default:
149	>	unrecognizedCommand(token);
150	>	return;
151	>	}
152		}
99	–	}
153
154	<	void SelectionEvaluator::predefine(const std::string& script) {
102	<	if (compiler.compile("#predefine", script)) {
103	<	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
104	<	if (aatoken.size() != 1) {
105	<	viewer.scriptStatus("predefinition does not have exactly 1 command:"
106	<	+ script);
107	<	return;
108	<	}
154	>	}
155
156	<	std::vector<Token> statement = aatoken[0];
157	<
158	<	if (statement.size() > 2) {
159	<	int tok = statement[1].tok;
160	<	if (tok == Token::identifier ||
161	<	(tok & Token::predefinedset) == Token::predefinedset) {
162	<	std::string variable = (std::string)statement[1].value;
163	<	variables.put(variable, statement);
164	<	} else {
165	<	viewer.scriptStatus("invalid variable name:" + script);
166	<	}
167	<	} else {
168	<	viewer.scriptStatus("bad predefinition length:" + script);
156	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){
157	>
158	>	while ( pc < aatoken.size()) {
159	>	statement = aatoken[pc++];
160	>	statementLength = statement.size();
161	>	Token token = statement[0];
162	>	switch (token.tok) {
163	>	case Token::define:
164	>	define();
165	>	break;
166	>	case Token::select:
167	>	select(bs, frame);
168	>	break;
169	>	default:
170	>	unrecognizedCommand(token);
171	>	return;
172		}
124	–	} else {
125	–	viewer.scriptStatus("predefined set compile error:" + script +
126	–	"\ncompile error:" + compiler.getErrorMessage());
173		}
174	+
175		}
176
177	<
178	<
179	<	BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
180	<	int numberOfAtoms = viewer.getAtomCount();
181	<	BitSet bs;
182	<	BitSet[] stack = new BitSet[10];
183	<	int sp = 0;
137	<
138	<	for (int pc = pcStart; ; ++pc) {
177	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
178	>	int pcStart) {
179	>	SelectionSet bs = createSelectionSets();
180	>	std::stack<SelectionSet> stack;
181	>	vector<int> bsSize = bs.size();
182	>
183	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
184		Token instruction = code[pc];
185	<	if (logMessages)
141	<	viewer.scriptStatus("instruction=" + instruction);
185	>
186		switch (instruction.tok) {
187		case Token::expressionBegin:
188		break;
189		case Token::expressionEnd:
190	<	break expression_loop;
190	>	break;
191		case Token::all:
192	<	bs = stack[sp++] = new BitSet(numberOfAtoms);
193	<	for (int i = numberOfAtoms; --i >= 0; )
150	<	bs.set(i);
192	>	bs = allInstruction();
193	>	stack.push(bs);
194		break;
195		case Token::none:
196	<	stack[sp++] = new BitSet();
196	>	bs = createSelectionSets();
197	>	stack.push(bs);
198		break;
199		case Token::opOr:
200	<	bs = stack[--sp];
201	<	stack[sp-1].or(bs);
200	>	bs= stack.top();
201	>	stack.pop();
202	>	stack.top() |= bs;
203		break;
204		case Token::opAnd:
205	<	bs = stack[--sp];
206	<	stack[sp-1].and(bs);
205	>	bs = stack.top();
206	>	stack.pop();
207	>	stack.top() &= bs;
208		break;
209		case Token::opNot:
210	<	bs = stack[sp - 1];
165	<	notSet(bs);
210	>	stack.top().flip();
211		break;
212		case Token::within:
213	<	bs = stack[sp - 1];
169	<	stack[sp - 1] = new BitSet();
170	<	withinInstruction(instruction, bs, stack[sp - 1]);
213	>	withinInstruction(instruction, stack.top());
214		break;
215	<	case Token::selected:
216	<	stack[sp++] = copyBitSet(viewer.getSelectionSet());
215	>	case Token::hull:
216	>	stack.push(hull());
217		break;
218	+	//case Token::selected:
219	+	//  stack.push(getSelectionSet());
220	+	//  break;
221		case Token::name:
222	<
222	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
223		break;
224	<	case  Token::index:
225	<
224	>	case Token::index:
225	>	stack.push(indexInstruction(instruction.value));
226		break;
181	–	case Token::molname:
182	–
183	–	break;
184	–	case Token::molindex:
185	–	break;
227		case Token::identifier:
228	<	stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
228	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
229		break;
230		case Token::opLT:
231		case Token::opLE:
#	Line 192 | Line 233 | void SelectionEvaluator::instructionDispatchLoop(){
233		case Token::opGT:
234		case Token::opEQ:
235		case Token::opNE:
236	<	bs = stack[sp++] = new BitSet();
196	<	comparatorInstruction(instruction, bs);
236	>	stack.push(comparatorInstruction(instruction));
237		break;
238		default:
239		unrecognizedExpression();
240		}
241		}
242	<	if (sp != 1)
242	>	if (stack.size() != 1)
243		evalError("atom expression compiler error - stack over/underflow");
244	<	return stack[0];
244	>
245	>	return stack.top();
246		}
247
248
249	<
250	<	void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
251	<	int comparator = instruction.tok;
252	<	int property = instruction.intValue;
253	<	float propertyValue = 0; // just for temperature
254	<	int comparisonValue = ((Integer)instruction.value).intValue();
255	<	int numberOfAtoms = viewer.getAtomCount();
215	<	Frame frame = viewer.getFrame();
216	<	for (int i = 0; i < numberOfAtoms; ++i) {
217	<	Atom atom = frame.getAtomAt(i);
218	<	switch (property) {
219	<	case Token::mass:
220	<	//propertyValue = atom.getAtomNumber();
221	<	break;
222	<	case Token::charge:
249	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
250	>	int pcStart, int frame) {
251	>	SelectionSet bs = createSelectionSets();
252	>	std::stack<SelectionSet> stack;
253	>
254	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
255	>	Token instruction = code[pc];
256
257	+	switch (instruction.tok) {
258	+	case Token::expressionBegin:
259		break;
260	<	case Token::dipole:
226	<
227	<	break;
228	<	default:
229	<	unrecognizedAtomProperty(property);
230	<	}
231	<	bool match = false;
232	<	switch (comparator) {
233	<	case Token::opLT:
234	<	match = propertyValue < comparisonValue;
260	>	case Token::expressionEnd:
261		break;
262	<	case Token::opLE:
263	<	match = propertyValue <= comparisonValue;
262	>	case Token::all:
263	>	bs = allInstruction();
264	>	stack.push(bs);
265		break;
266	<	case Token::opGE:
267	<	match = propertyValue >= comparisonValue;
266	>	case Token::none:
267	>	bs = SelectionSet(nObjects);
268	>	stack.push(bs);
269		break;
270	<	case Token::opGT:
271	<	match = propertyValue > comparisonValue;
270	>	case Token::opOr:
271	>	bs = stack.top();
272	>	stack.pop();
273	>	stack.top() |= bs;
274		break;
275	<	case Token::opEQ:
276	<	match = propertyValue == comparisonValue;
275	>	case Token::opAnd:
276	>	bs = stack.top();
277	>	stack.pop();
278	>	stack.top() &= bs;
279		break;
280	+	case Token::opNot:
281	+	stack.top().flip();
282	+	break;
283	+	case Token::within:
284	+	withinInstruction(instruction, stack.top(), frame);
285	+	break;
286	+	case Token::hull:
287	+	stack.push(hull(frame));
288	+	break;
289	+	//case Token::selected:
290	+	//  stack.push(getSelectionSet());
291	+	//  break;
292	+	case Token::name:
293	+	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
294	+	break;
295	+	case Token::index:
296	+	stack.push(indexInstruction(instruction.value));
297	+	break;
298	+	case Token::identifier:
299	+	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
300	+	break;
301	+	case Token::opLT:
302	+	case Token::opLE:
303	+	case Token::opGE:
304	+	case Token::opGT:
305	+	case Token::opEQ:
306		case Token::opNE:
307	<	match = propertyValue != comparisonValue;
307	>	stack.push(comparatorInstruction(instruction, frame));
308		break;
309	+	default:
310	+	unrecognizedExpression();
311		}
252	–	if (match)
253	–	bs.set(i);
312		}
313	+	if (stack.size() != 1)
314	+	evalError("atom expression compiler error - stack over/underflow");
315	+
316	+	return stack.top();
317		}
318
257	–	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
319
259	–	boost::any withinSpec = instruction.value;
260	–	if (withinSpec instanceof Float) {
261	–	withinDistance(((Float)withinSpec).floatValue(), bs, bsResult);
262	–	return;
263	–	}
264	–	evalError("Unrecognized within parameter:" + withinSpec);
265	–	}
320
321	<	void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) {
322	<	Frame frame = viewer.getFrame();
323	<	for (int i = frame.getAtomCount(); --i >= 0; ) {
324	<	if (bs.get(i)) {
325	<	Atom atom = frame.getAtomAt(i);
326	<	AtomIterator iterWithin =
327	<	frame.getWithinIterator(atom, distance);
328	<	while (iterWithin.hasNext())
329	<	bsResult.set(iterWithin.next().getAtomIndex());
321	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
322	>	int comparator = instruction.tok;
323	>	int property = instruction.intValue;
324	>	float comparisonValue = boost::any_cast<float>(instruction.value);
325	>	SelectionSet bs = createSelectionSets();
326	>	bs.clearAll();
327	>
328	>	SimInfo::MoleculeIterator mi;
329	>	Molecule* mol;
330	>	Molecule::AtomIterator ai;
331	>	Atom* atom;
332	>	Molecule::RigidBodyIterator rbIter;
333	>	RigidBody* rb;
334	>
335	>	for (mol = info->beginMolecule(mi); mol != NULL;
336	>	mol = info->nextMolecule(mi)) {
337	>
338	>	compareProperty(mol, bs, property, comparator, comparisonValue);
339	>
340	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
341	>	compareProperty(atom, bs, property, comparator, comparisonValue);
342		}
343	+
344	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
345	+	rb = mol->nextRigidBody(rbIter)) {
346	+	compareProperty(rb, bs, property, comparator, comparisonValue);
347	+	}
348		}
278	–	}
349
350	<	void SelectionEvaluator::define() {
281	<	std::string variable = (std::string)statement[1].value;
282	<	variables.insert(std::make_pair(variable, expression(statement, 2)));
350	>	return bs;
351		}
284	–	}
352
353	<	void SelectionEvaluator::predefine(Token[] statement) {
354	<	std::string variable = (std::string)statement[1].value;
355	<	variables.put(variable, statement);
353	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
354	>	int comparator = instruction.tok;
355	>	int property = instruction.intValue;
356	>	float comparisonValue = boost::any_cast<float>(instruction.value);
357	>	SelectionSet bs = createSelectionSets();
358	>	bs.clearAll();
359	>
360	>	SimInfo::MoleculeIterator mi;
361	>	Molecule* mol;
362	>	Molecule::AtomIterator ai;
363	>	Atom* atom;
364	>	Molecule::RigidBodyIterator rbIter;
365	>	RigidBody* rb;
366	>
367	>	for (mol = info->beginMolecule(mi); mol != NULL;
368	>	mol = info->nextMolecule(mi)) {
369	>
370	>	compareProperty(mol, bs, property, comparator, comparisonValue, frame);
371	>
372	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
373	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
374	>	}
375	>
376	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
377	>	rb = mol->nextRigidBody(rbIter)) {
378	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
379	>	}
380	>	}
381	>
382	>	return bs;
383		}
384
385	<	void SelectionEvaluator::select(){
386	<	viewer.setSelectionSet(expression(statement, 1));
385	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
386	>	int property, int comparator,
387	>	float comparisonValue) {
388	>	RealType propertyValue = 0.0;
389	>	Vector3d pos;
390	>
391	>	switch (property) {
392	>	case Token::mass:
393	>	propertyValue = sd->getMass();
394	>	break;
395	>	case Token::charge:
396	>	if (sd->isAtom()){
397	>	Atom* atom = static_cast<Atom*>(sd);
398	>	propertyValue = getCharge(atom);
399	>	} else if (sd->isRigidBody()) {
400	>	RigidBody* rb = static_cast<RigidBody*>(sd);
401	>	RigidBody::AtomIterator ai;
402	>	Atom* atom;
403	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
404	>	propertyValue+=  getCharge(atom);
405	>	}
406	>	}
407	>	break;
408	>	case Token::x:
409	>	propertyValue = sd->getPos().x();
410	>	break;
411	>	case Token::y:
412	>	propertyValue = sd->getPos().y();
413	>	break;
414	>	case Token::z:
415	>	propertyValue = sd->getPos().z();
416	>	break;
417	>	case Token::wrappedX:
418	>	pos = sd->getPos();
419	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
420	>	propertyValue = pos.x();
421	>	break;
422	>	case Token::wrappedY:
423	>	pos = sd->getPos();
424	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
425	>	propertyValue = pos.y();
426	>	break;
427	>	case Token::wrappedZ:
428	>	pos = sd->getPos();
429	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
430	>	propertyValue = pos.z();
431	>	break;
432	>	case Token::r:
433	>	propertyValue = sd->getPos().length();
434	>	break;
435	>	default:
436	>	unrecognizedAtomProperty(property);
437	>	}
438	>
439	>	bool match = false;
440	>	switch (comparator) {
441	>	case Token::opLT:
442	>	match = propertyValue < comparisonValue;
443	>	break;
444	>	case Token::opLE:
445	>	match = propertyValue <= comparisonValue;
446	>	break;
447	>	case Token::opGE:
448	>	match = propertyValue >= comparisonValue;
449	>	break;
450	>	case Token::opGT:
451	>	match = propertyValue > comparisonValue;
452	>	break;
453	>	case Token::opEQ:
454	>	match = propertyValue == comparisonValue;
455	>	break;
456	>	case Token::opNE:
457	>	match = propertyValue != comparisonValue;
458	>	break;
459	>	}
460	>
461	>	if (match)
462	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
463	>
464	>
465		}
466	+
467	+	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
468	+	int property, int comparator,
469	+	float comparisonValue) {
470	+	RealType propertyValue = 0.0;
471	+	Vector3d pos;
472	+
473	+	switch (property) {
474	+	case Token::mass:
475	+	propertyValue = mol->getMass();
476	+	break;
477	+	case Token::charge:
478	+	{
479	+	Molecule::AtomIterator ai;
480	+	Atom* atom;
481	+	for (atom = mol->beginAtom(ai); atom != NULL;
482	+	atom = mol->nextAtom(ai)) {
483	+	propertyValue+=  getCharge(atom);
484	+	}
485	+	}
486	+	break;
487	+	case Token::x:
488	+	propertyValue = mol->getCom().x();
489	+	break;
490	+	case Token::y:
491	+	propertyValue = mol->getCom().y();
492	+	break;
493	+	case Token::z:
494	+	propertyValue = mol->getCom().z();
495	+	break;
496	+	case Token::wrappedX:
497	+	pos = mol->getCom();
498	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
499	+	propertyValue = pos.x();
500	+	break;
501	+	case Token::wrappedY:
502	+	pos = mol->getCom();
503	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
504	+	propertyValue = pos.y();
505	+	break;
506	+	case Token::wrappedZ:
507	+	pos = mol->getCom();
508	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
509	+	propertyValue = pos.z();
510	+	break;
511	+	case Token::r:
512	+	propertyValue = mol->getCom().length();
513	+	break;
514	+	default:
515	+	unrecognizedMoleculeProperty(property);
516	+	}
517	+
518	+	bool match = false;
519	+	switch (comparator) {
520	+	case Token::opLT:
521	+	match = propertyValue < comparisonValue;
522	+	break;
523	+	case Token::opLE:
524	+	match = propertyValue <= comparisonValue;
525	+	break;
526	+	case Token::opGE:
527	+	match = propertyValue >= comparisonValue;
528	+	break;
529	+	case Token::opGT:
530	+	match = propertyValue > comparisonValue;
531	+	break;
532	+	case Token::opEQ:
533	+	match = propertyValue == comparisonValue;
534	+	break;
535	+	case Token::opNE:
536	+	match = propertyValue != comparisonValue;
537	+	break;
538	+	}
539	+
540	+	if (match)
541	+	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
542	+	}
543	+
544	+	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
545	+	int property, int comparator,
546	+	float comparisonValue, int frame) {
547	+	RealType propertyValue = 0.0;
548	+	Vector3d pos;
549	+	switch (property) {
550	+	case Token::mass:
551	+	propertyValue = mol->getMass();
552	+	break;
553	+	case Token::charge:
554	+	{
555	+	Molecule::AtomIterator ai;
556	+	Atom* atom;
557	+	for (atom = mol->beginAtom(ai); atom != NULL;
558	+	atom = mol->nextAtom(ai)) {
559	+	propertyValue+=  getCharge(atom,frame);
560	+	}
561	+	}
562	+	break;
563	+	case Token::x:
564	+	propertyValue = mol->getCom(frame).x();
565	+	break;
566	+	case Token::y:
567	+	propertyValue = mol->getCom(frame).y();
568	+	break;
569	+	case Token::z:
570	+	propertyValue = mol->getCom(frame).z();
571	+	break;
572	+	case Token::wrappedX:
573	+	pos = mol->getCom(frame);
574	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
575	+	propertyValue = pos.x();
576	+	break;
577	+	case Token::wrappedY:
578	+	pos = mol->getCom(frame);
579	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
580	+	propertyValue = pos.y();
581	+	break;
582	+	case Token::wrappedZ:
583	+	pos = mol->getCom(frame);
584	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
585	+	propertyValue = pos.z();
586	+	break;
587	+
588	+	case Token::r:
589	+	propertyValue = mol->getCom(frame).length();
590	+	break;
591	+	default:
592	+	unrecognizedMoleculeProperty(property);
593	+	}
594	+
595	+	bool match = false;
596	+	switch (comparator) {
597	+	case Token::opLT:
598	+	match = propertyValue < comparisonValue;
599	+	break;
600	+	case Token::opLE:
601	+	match = propertyValue <= comparisonValue;
602	+	break;
603	+	case Token::opGE:
604	+	match = propertyValue >= comparisonValue;
605	+	break;
606	+	case Token::opGT:
607	+	match = propertyValue > comparisonValue;
608	+	break;
609	+	case Token::opEQ:
610	+	match = propertyValue == comparisonValue;
611	+	break;
612	+	case Token::opNE:
613	+	match = propertyValue != comparisonValue;
614	+	break;
615	+	}
616	+	if (match)
617	+	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
618	+
619	+
620	+	}
621	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
622	+	int property, int comparator,
623	+	float comparisonValue, int frame) {
624	+	RealType propertyValue = 0.0;
625	+	Vector3d pos;
626	+	switch (property) {
627	+	case Token::mass:
628	+	propertyValue = sd->getMass();
629	+	break;
630	+	case Token::charge:
631	+	if (sd->isAtom()){
632	+	Atom* atom = static_cast<Atom*>(sd);
633	+	propertyValue = getCharge(atom,frame);
634	+	} else if (sd->isRigidBody()) {
635	+	RigidBody* rb = static_cast<RigidBody*>(sd);
636	+	RigidBody::AtomIterator ai;
637	+	Atom* atom;
638	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
639	+	propertyValue+=  getCharge(atom,frame);
640	+	}
641	+	}
642	+	break;
643	+	case Token::x:
644	+	propertyValue = sd->getPos(frame).x();
645	+	break;
646	+	case Token::y:
647	+	propertyValue = sd->getPos(frame).y();
648	+	break;
649	+	case Token::z:
650	+	propertyValue = sd->getPos(frame).z();
651	+	break;
652	+	case Token::wrappedX:
653	+	pos = sd->getPos(frame);
654	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
655	+	propertyValue = pos.x();
656	+	break;
657	+	case Token::wrappedY:
658	+	pos = sd->getPos(frame);
659	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
660	+	propertyValue = pos.y();
661	+	break;
662	+	case Token::wrappedZ:
663	+	pos = sd->getPos(frame);
664	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
665	+	propertyValue = pos.z();
666	+	break;
667	+
668	+	case Token::r:
669	+	propertyValue = sd->getPos(frame).length();
670	+	break;
671	+	default:
672	+	unrecognizedAtomProperty(property);
673	+	}
674	+
675	+	bool match = false;
676	+	switch (comparator) {
677	+	case Token::opLT:
678	+	match = propertyValue < comparisonValue;
679	+	break;
680	+	case Token::opLE:
681	+	match = propertyValue <= comparisonValue;
682	+	break;
683	+	case Token::opGE:
684	+	match = propertyValue >= comparisonValue;
685	+	break;
686	+	case Token::opGT:
687	+	match = propertyValue > comparisonValue;
688	+	break;
689	+	case Token::opEQ:
690	+	match = propertyValue == comparisonValue;
691	+	break;
692	+	case Token::opNE:
693	+	match = propertyValue != comparisonValue;
694	+	break;
695	+	}
696	+	if (match)
697	+	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
698	+
699	+
700	+	}
701	+
702
703	<	}
703	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
704	>	SelectionSet& bs){
705	>
706	>	boost::any withinSpec = instruction.value;
707	>	float distance;
708	>	if (withinSpec.type() == typeid(float)){
709	>	distance = boost::any_cast<float>(withinSpec);
710	>	} else if (withinSpec.type() == typeid(int)) {
711	>	distance = boost::any_cast<int>(withinSpec);
712	>	} else {
713	>	evalError("casting error in withinInstruction");
714	>	bs.clearAll();
715	>	}
716	>
717	>	bs = distanceFinder.find(bs, distance);
718	>	}
719	>
720	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
721	>	SelectionSet& bs, int frame){
722	>
723	>	boost::any withinSpec = instruction.value;
724	>	float distance;
725	>	if (withinSpec.type() == typeid(float)){
726	>	distance = boost::any_cast<float>(withinSpec);
727	>	} else if (withinSpec.type() == typeid(int)) {
728	>	distance = boost::any_cast<int>(withinSpec);
729	>	} else {
730	>	evalError("casting error in withinInstruction");
731	>	bs.clearAll();
732	>	}
733	>
734	>	bs = distanceFinder.find(bs, distance, frame);
735	>	}
736	>
737	>	void SelectionEvaluator::define() {
738	>	assert(statement.size() >= 3);
739	>
740	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
741	>
742	>	variables.insert(VariablesType::value_type(variable,
743	>	expression(statement, 2)));
744	>	}
745	>
746	>
747	>	/** @todo */
748	>	void SelectionEvaluator::predefine(const std::string& script) {
749	>
750	>	if (compiler.compile("#predefine", script)) {
751	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
752	>	if (aatoken.size() != 1) {
753	>	evalError("predefinition does not have exactly 1 command:"
754	>	+ script);
755	>	return;
756	>	}
757	>	std::vector<Token> statement = aatoken[0];
758	>	if (statement.size() > 2) {
759	>	int tok = statement[1].tok;
760	>	if (tok == Token::identifier ||
761	>	(tok & Token::predefinedset) == Token::predefinedset) {
762	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
763	>	variables.insert(VariablesType::value_type(variable, statement));
764	>
765	>	} else {
766	>	evalError("invalid variable name:" + script);
767	>	}
768	>	}else {
769	>	evalError("bad predefinition length:" + script);
770	>	}
771	>
772	>	} else {
773	>	evalError("predefined set compile error:" + script +
774	>	"\ncompile error:" + compiler.getErrorMessage());
775	>	}
776	>	}
777	>
778	>	void SelectionEvaluator::select(SelectionSet& bs){
779	>	bs = expression(statement, 1);
780	>	}
781	>
782	>	void SelectionEvaluator::select(SelectionSet& bs, int frame){
783	>	bs = expression(statement, 1, frame);
784	>	}
785	>
786	>	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
787	>
788	>	SelectionSet bs = createSelectionSets();
789	>	std::map<std::string, boost::any>::iterator i = variables.find(variable);
790	>
791	>	if (i != variables.end()) {
792	>	if (i->second.type() == typeid(SelectionSet)) {
793	>	return boost::any_cast<SelectionSet>(i->second);
794	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
795	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
796	>	i->second =  bs; /**@todo fixme */
797	>	return bs;
798	>	}
799	>	} else {
800	>	unrecognizedIdentifier(variable);
801	>	}
802	>
803	>	return bs;
804	>	}
805	>
806	>	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
807	>	return nameFinder.match(name);
808	>	}
809	>
810	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
811	>	std::vector<Token>::const_iterator i;
812	>	for (i = tokens.begin(); i != tokens.end(); ++i) {
813	>	if (i->tok & Token::dynamic) {
814	>	return true;
815	>	}
816	>	}
817	>
818	>	return false;
819	>	}
820	>
821	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
822	>	variables.clear();
823	>	//load predefine
824	>	//predefine();
825	>	}
826	>
827	>	SelectionSet SelectionEvaluator::createSelectionSets() {
828	>	SelectionSet ss(nObjects);
829	>	return ss;
830	>	}
831	>
832	>	SelectionSet SelectionEvaluator::evaluate() {
833	>	SelectionSet bs = createSelectionSets();
834	>	if (isLoaded_) {
835	>	pc = 0;
836	>	instructionDispatchLoop(bs);
837	>	}
838	>	return bs;
839	>	}
840	>
841	>	SelectionSet SelectionEvaluator::evaluate(int frame) {
842	>	SelectionSet bs = createSelectionSets();
843	>	if (isLoaded_) {
844	>	pc = 0;
845	>	instructionDispatchLoop(bs, frame);
846	>	}
847	>	return bs;
848	>	}
849	>
850	>	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
851	>	SelectionSet bs = createSelectionSets();
852	>
853	>	if (value.type() == typeid(int)) {
854	>	int index = boost::any_cast<int>(value);
855	>	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
856	>	invalidIndex(index);
857	>	} else {
858	>	bs = indexFinder.find(index);
859	>	}
860	>	} else if (value.type() == typeid(std::pair<int, int>)) {
861	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
862	>	assert(indexRange.first <= indexRange.second);
863	>	if (indexRange.first < 0 ||
864	>	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
865	>	invalidIndexRange(indexRange);
866	>	}else {
867	>	bs = indexFinder.find(indexRange.first, indexRange.second);
868	>	}
869	>	}
870	>
871	>	return bs;
872	>	}
873	>
874	>	SelectionSet SelectionEvaluator::allInstruction() {
875	>	SelectionSet ss = createSelectionSets();
876	>
877	>	SimInfo::MoleculeIterator mi;
878	>	Molecule::AtomIterator ai;
879	>	Molecule::RigidBodyIterator rbIter;
880	>	Molecule::BondIterator bondIter;
881	>	Molecule::BendIterator bendIter;
882	>	Molecule::TorsionIterator torsionIter;
883	>	Molecule::InversionIterator inversionIter;
884	>
885	>	Molecule* mol;
886	>	Atom* atom;
887	>	RigidBody* rb;
888	>	Bond* bond;
889	>	Bend* bend;
890	>	Torsion* torsion;
891	>	Inversion* inversion;
892	>
893	>	// Doing the loop insures that we're actually on this processor.
894	>
895	>	for (mol = info->beginMolecule(mi); mol != NULL;
896	>	mol = info->nextMolecule(mi)) {
897	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
898	>	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
899	>	}
900	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
901	>	rb = mol->nextRigidBody(rbIter)) {
902	>	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
903	>	}
904	>	for (bond = mol->beginBond(bondIter); bond != NULL;
905	>	bond = mol->nextBond(bondIter)) {
906	>	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
907	>	}
908	>	for (bend = mol->beginBend(bendIter); bend != NULL;
909	>	bend = mol->nextBend(bendIter)) {
910	>	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
911	>	}
912	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
913	>	torsion = mol->nextTorsion(torsionIter)) {
914	>	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
915	>	}
916	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
917	>	inversion = mol->nextInversion(inversionIter)) {
918	>	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
919	>	}
920	>	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
921	>	}
922	>
923	>	return ss;
924	>	}
925	>
926	>	SelectionSet SelectionEvaluator::hull() {
927	>	SelectionSet bs = createSelectionSets();
928	>
929	>	bs = hullFinder.findHull();
930	>	surfaceArea_ = hullFinder.getSurfaceArea();
931	>	hasSurfaceArea_ = true;
932	>	return bs;
933	>	}
934	>
935	>
936	>	SelectionSet SelectionEvaluator::hull(int frame) {
937	>	SelectionSet bs = createSelectionSets();
938	>
939	>	bs = hullFinder.findHull(frame);
940	>
941	>	return bs;
942	>	}
943	>
944	>	RealType SelectionEvaluator::getCharge(Atom* atom) {
945	>	RealType charge = 0.0;
946	>	AtomType* atomType = atom->getAtomType();
947	>
948	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
949	>	if ( fca.isFixedCharge() ) {
950	>	charge = fca.getCharge();
951	>	}
952	>
953	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
954	>	if ( fqa.isFluctuatingCharge() ) {
955	>	charge += atom->getFlucQPos();
956	>	}
957	>	return charge;
958	>	}
959	>
960	>	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
961	>	RealType charge = 0.0;
962	>	AtomType* atomType = atom->getAtomType();
963	>
964	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
965	>	if ( fca.isFixedCharge() ) {
966	>	charge = fca.getCharge();
967	>	}
968	>
969	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
970	>	if ( fqa.isFluctuatingCharge() ) {
971	>	charge += atom->getFlucQPos(frame);
972	>	}
973	>	return charge;
974	>	}
975	>
976	>	}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 281 by tim, Wed Feb 2 23:13:11 2005 UTC vs.
Revision 2055 by gezelter, Fri Feb 6 18:49:27 2015 UTC

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