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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 2071 by gezelter, Sat Mar 7 21:41:51 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	>	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
57	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
58	>	indexFinder(info), isLoaded_(false), hasSurfaceArea_(false) {
59	>	nObjects.push_back(info->getNGlobalAtoms() + info->getNGlobalRigidBodies());
60	>	nObjects.push_back(info->getNGlobalBonds());
61	>	nObjects.push_back(info->getNGlobalBends());
62	>	nObjects.push_back(info->getNGlobalTorsions());
63	>	nObjects.push_back(info->getNGlobalInversions());
64	>	nObjects.push_back(info->getNGlobalMolecules());
65	>	}
66	>
67	>	bool SelectionEvaluator::loadScript(const std::string& filename,
68	>	const std::string& script) {
69	>	clearDefinitionsAndLoadPredefined();
70		this->filename = filename;
71		this->script = script;
72		if (! compiler.compile(filename, script)) {
73	<	error = true;
74	<	errorMessage = compiler.getErrorMessage();
75	<	return false;
73	>	error = true;
74	>	errorMessage = compiler.getErrorMessage();
75	>
76	>	sprintf( painCave.errMsg,
77	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
78	>	painCave.severity = OPENMD_ERROR;
79	>	painCave.isFatal = 1;
80	>	simError();
81	>	return false;
82		}
83
84		pc = 0;
85		aatoken = compiler.getAatokenCompiled();
86		linenumbers = compiler.getLineNumbers();
87		lineIndices = compiler.getLineIndices();
88	+
89	+	std::vector<std::vector<Token> >::const_iterator i;
90	+
91	+	isDynamic_ = false;
92	+	for (i = aatoken.begin(); i != aatoken.end(); ++i) {
93	+	if (containDynamicToken(*i)) {
94	+	isDynamic_ = true;
95	+	break;
96	+	}
97	+	}
98	+
99	+	isLoaded_ = true;
100		return true;
101	<	}
101	>	}
102
103	<	void SelectionEvaluator::clearState() {
63	<	for (int i = scriptLevelMax; --i >= 0; )
64	<	stack[i].clear();
65	<	scriptLevel = 0;
103	>	void SelectionEvaluator::clearState() {
104		error = false;
105		errorMessage = "";
106	<	}
106	>	}
107
108	<	bool SelectionEvaluator::loadScriptString(const std::string& script) {
108	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
109		clearState();
110		return loadScript("", script);
111	<	}
111	>	}
112
113	<	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
113	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
114		clearState();
115		return loadScriptFileInternal(filename);
116	<	}
116	>	}
117
118	<
119	<	void SelectionEvaluator::instructionDispatchLoop(){
120	<
118	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
119	>	ifstrstream ifs(filename.c_str());
120	>	if (!ifs.is_open()) {
121	>	return false;
122	>	}
123	>
124	>	const int bufferSize = 65535;
125	>	char buffer[bufferSize];
126	>	std::string script;
127	>	while(ifs.getline(buffer, bufferSize)) {
128	>	script += buffer;
129	>	}
130	>	return loadScript(filename, script);
131	>	}
132	>
133	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){
134	>
135		while ( pc < aatoken.size()) {
136	<	statement = aatoken[pc++];
137	<	statementLength = statement.size();
138	<	Token token = statement[0];
139	<	switch (token.tok) {
140	<	case Token::define:
141	<	define();
142	<	break;
143	<	case Token::select:
144	<	select();
145	<	break;
146	<	default:
147	<	unrecognizedCommand(token);
148	<	return;
149	<	}
136	>	statement = aatoken[pc++];
137	>	statementLength = statement.size();
138	>	Token token = statement[0];
139	>	switch (token.tok) {
140	>	case Token::define:
141	>	define();
142	>	break;
143	>	case Token::select:
144	>	select(bs);
145	>	break;
146	>	default:
147	>	unrecognizedCommand(token);
148	>	return;
149	>	}
150		}
99	–	}
151
152	<	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	<	}
152	>	}
153
154	<	std::vector<Token> statement = aatoken[0];
155	<
156	<	if (statement.size() > 2) {
157	<	int tok = statement[1].tok;
158	<	if (tok == Token::identifier ||
159	<	(tok & Token::predefinedset) == Token::predefinedset) {
160	<	std::string variable = (std::string)statement[1].value;
161	<	variables.put(variable, statement);
162	<	} else {
163	<	viewer.scriptStatus("invalid variable name:" + script);
164	<	}
165	<	} else {
166	<	viewer.scriptStatus("bad predefinition length:" + script);
154	>	void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){
155	>
156	>	while ( pc < aatoken.size()) {
157	>	statement = aatoken[pc++];
158	>	statementLength = statement.size();
159	>	Token token = statement[0];
160	>	switch (token.tok) {
161	>	case Token::define:
162	>	define();
163	>	break;
164	>	case Token::select:
165	>	select(bs, frame);
166	>	break;
167	>	default:
168	>	unrecognizedCommand(token);
169	>	return;
170		}
124	–	} else {
125	–	viewer.scriptStatus("predefined set compile error:" + script +
126	–	"\ncompile error:" + compiler.getErrorMessage());
171		}
172	+
173		}
174
175	<
176	<
177	<	BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
178	<	int numberOfAtoms = viewer.getAtomCount();
179	<	BitSet bs;
180	<	BitSet[] stack = new BitSet[10];
181	<	int sp = 0;
137	<
138	<	for (int pc = pcStart; ; ++pc) {
175	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
176	>	int pcStart) {
177	>	SelectionSet bs = createSelectionSets();
178	>	std::stack<SelectionSet> stack;
179	>	vector<int> bsSize = bs.size();
180	>
181	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
182		Token instruction = code[pc];
183	<	if (logMessages)
141	<	viewer.scriptStatus("instruction=" + instruction);
183	>
184		switch (instruction.tok) {
185		case Token::expressionBegin:
186		break;
187		case Token::expressionEnd:
188	<	break expression_loop;
188	>	break;
189		case Token::all:
190	<	bs = stack[sp++] = new BitSet(numberOfAtoms);
191	<	for (int i = numberOfAtoms; --i >= 0; )
150	<	bs.set(i);
190	>	bs = allInstruction();
191	>	stack.push(bs);
192		break;
193		case Token::none:
194	<	stack[sp++] = new BitSet();
194	>	bs = createSelectionSets();
195	>	stack.push(bs);
196		break;
197		case Token::opOr:
198	<	bs = stack[--sp];
199	<	stack[sp-1].or(bs);
198	>	bs= stack.top();
199	>	stack.pop();
200	>	stack.top() |= bs;
201		break;
202		case Token::opAnd:
203	<	bs = stack[--sp];
204	<	stack[sp-1].and(bs);
203	>	bs = stack.top();
204	>	stack.pop();
205	>	stack.top() &= bs;
206		break;
207		case Token::opNot:
208	<	bs = stack[sp - 1];
165	<	notSet(bs);
208	>	stack.top().flip();
209		break;
210		case Token::within:
211	<	bs = stack[sp - 1];
169	<	stack[sp - 1] = new BitSet();
170	<	withinInstruction(instruction, bs, stack[sp - 1]);
211	>	withinInstruction(instruction, stack.top());
212		break;
213	<	case Token::selected:
214	<	stack[sp++] = copyBitSet(viewer.getSelectionSet());
213	>	case Token::hull:
214	>	stack.push(hull());
215		break;
216	+	//case Token::selected:
217	+	//  stack.push(getSelectionSet());
218	+	//  break;
219		case Token::name:
220	<
220	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
221		break;
222	<	case  Token::index:
223	<
222	>	case Token::index:
223	>	stack.push(indexInstruction(instruction.value));
224		break;
181	–	case Token::molname:
182	–
183	–	break;
184	–	case Token::molindex:
185	–	break;
225		case Token::identifier:
226	<	stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
226	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
227		break;
228		case Token::opLT:
229		case Token::opLE:
#	Line 192 | Line 231 | void SelectionEvaluator::instructionDispatchLoop(){
231		case Token::opGT:
232		case Token::opEQ:
233		case Token::opNE:
234	<	bs = stack[sp++] = new BitSet();
196	<	comparatorInstruction(instruction, bs);
234	>	stack.push(comparatorInstruction(instruction));
235		break;
236		default:
237		unrecognizedExpression();
238		}
239		}
240	<	if (sp != 1)
240	>	if (stack.size() != 1)
241		evalError("atom expression compiler error - stack over/underflow");
242	<	return stack[0];
242	>
243	>	return stack.top();
244		}
245
246
247	<
248	<	void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
249	<	int comparator = instruction.tok;
250	<	int property = instruction.intValue;
251	<	float propertyValue = 0; // just for temperature
252	<	int comparisonValue = ((Integer)instruction.value).intValue();
253	<	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:
247	>	SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
248	>	int pcStart, int frame) {
249	>	SelectionSet bs = createSelectionSets();
250	>	std::stack<SelectionSet> stack;
251	>
252	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
253	>	Token instruction = code[pc];
254
255	+	switch (instruction.tok) {
256	+	case Token::expressionBegin:
257		break;
258	<	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;
258	>	case Token::expressionEnd:
259		break;
260	<	case Token::opLE:
261	<	match = propertyValue <= comparisonValue;
260	>	case Token::all:
261	>	bs = allInstruction();
262	>	stack.push(bs);
263		break;
264	<	case Token::opGE:
265	<	match = propertyValue >= comparisonValue;
264	>	case Token::none:
265	>	bs = SelectionSet(nObjects);
266	>	stack.push(bs);
267		break;
268	<	case Token::opGT:
269	<	match = propertyValue > comparisonValue;
268	>	case Token::opOr:
269	>	bs = stack.top();
270	>	stack.pop();
271	>	stack.top() |= bs;
272		break;
273	<	case Token::opEQ:
274	<	match = propertyValue == comparisonValue;
273	>	case Token::opAnd:
274	>	bs = stack.top();
275	>	stack.pop();
276	>	stack.top() &= bs;
277		break;
278	+	case Token::opNot:
279	+	stack.top().flip();
280	+	break;
281	+	case Token::within:
282	+	withinInstruction(instruction, stack.top(), frame);
283	+	break;
284	+	case Token::hull:
285	+	stack.push(hull(frame));
286	+	break;
287	+	//case Token::selected:
288	+	//  stack.push(getSelectionSet());
289	+	//  break;
290	+	case Token::name:
291	+	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
292	+	break;
293	+	case Token::index:
294	+	stack.push(indexInstruction(instruction.value));
295	+	break;
296	+	case Token::identifier:
297	+	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
298	+	break;
299	+	case Token::opLT:
300	+	case Token::opLE:
301	+	case Token::opGE:
302	+	case Token::opGT:
303	+	case Token::opEQ:
304		case Token::opNE:
305	<	match = propertyValue != comparisonValue;
305	>	stack.push(comparatorInstruction(instruction, frame));
306		break;
307	+	default:
308	+	unrecognizedExpression();
309		}
252	–	if (match)
253	–	bs.set(i);
310		}
311	+	if (stack.size() != 1)
312	+	evalError("atom expression compiler error - stack over/underflow");
313	+
314	+	return stack.top();
315		}
316
257	–	void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
317
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	–	}
318
319	<	void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) {
320	<	Frame frame = viewer.getFrame();
321	<	for (int i = frame.getAtomCount(); --i >= 0; ) {
322	<	if (bs.get(i)) {
323	<	Atom atom = frame.getAtomAt(i);
324	<	AtomIterator iterWithin =
325	<	frame.getWithinIterator(atom, distance);
326	<	while (iterWithin.hasNext())
327	<	bsResult.set(iterWithin.next().getAtomIndex());
319	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
320	>	int comparator = instruction.tok;
321	>	int property = instruction.intValue;
322	>	float comparisonValue = boost::any_cast<float>(instruction.value);
323	>	SelectionSet bs = createSelectionSets();
324	>	bs.clearAll();
325	>
326	>	SimInfo::MoleculeIterator mi;
327	>	Molecule* mol;
328	>	Molecule::AtomIterator ai;
329	>	Atom* atom;
330	>	Molecule::RigidBodyIterator rbIter;
331	>	RigidBody* rb;
332	>
333	>	for (mol = info->beginMolecule(mi); mol != NULL;
334	>	mol = info->nextMolecule(mi)) {
335	>
336	>	compareProperty(mol, bs, property, comparator, comparisonValue);
337	>
338	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
339	>	compareProperty(atom, bs, property, comparator, comparisonValue);
340		}
341	+
342	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
343	+	rb = mol->nextRigidBody(rbIter)) {
344	+	compareProperty(rb, bs, property, comparator, comparisonValue);
345	+	}
346		}
278	–	}
347
348	<	void SelectionEvaluator::define() {
281	<	std::string variable = (std::string)statement[1].value;
282	<	variables.insert(std::make_pair(variable, expression(statement, 2)));
348	>	return bs;
349		}
284	–	}
350
351	<	void SelectionEvaluator::predefine(Token[] statement) {
352	<	std::string variable = (std::string)statement[1].value;
353	<	variables.put(variable, statement);
351	>	SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
352	>	int comparator = instruction.tok;
353	>	int property = instruction.intValue;
354	>	float comparisonValue = boost::any_cast<float>(instruction.value);
355	>	SelectionSet bs = createSelectionSets();
356	>	bs.clearAll();
357	>
358	>	SimInfo::MoleculeIterator mi;
359	>	Molecule* mol;
360	>	Molecule::AtomIterator ai;
361	>	Atom* atom;
362	>	Molecule::RigidBodyIterator rbIter;
363	>	RigidBody* rb;
364	>
365	>	for (mol = info->beginMolecule(mi); mol != NULL;
366	>	mol = info->nextMolecule(mi)) {
367	>
368	>	compareProperty(mol, bs, property, comparator, comparisonValue, frame);
369	>
370	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
371	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
372	>	}
373	>
374	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
375	>	rb = mol->nextRigidBody(rbIter)) {
376	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
377	>	}
378	>	}
379	>
380	>	return bs;
381		}
382
383	<	void SelectionEvaluator::select(){
384	<	viewer.setSelectionSet(expression(statement, 1));
383	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
384	>	int property, int comparator,
385	>	float comparisonValue) {
386	>	RealType propertyValue = 0.0;
387	>	Vector3d pos;
388	>
389	>	switch (property) {
390	>	case Token::mass:
391	>	propertyValue = sd->getMass();
392	>	break;
393	>	case Token::charge:
394	>	if (sd->isAtom()){
395	>	Atom* atom = static_cast<Atom*>(sd);
396	>	propertyValue = getCharge(atom);
397	>	} else if (sd->isRigidBody()) {
398	>	RigidBody* rb = static_cast<RigidBody*>(sd);
399	>	RigidBody::AtomIterator ai;
400	>	Atom* atom;
401	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
402	>	propertyValue+=  getCharge(atom);
403	>	}
404	>	}
405	>	break;
406	>	case Token::x:
407	>	propertyValue = sd->getPos().x();
408	>	break;
409	>	case Token::y:
410	>	propertyValue = sd->getPos().y();
411	>	break;
412	>	case Token::z:
413	>	propertyValue = sd->getPos().z();
414	>	break;
415	>	case Token::wrappedX:
416	>	pos = sd->getPos();
417	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
418	>	propertyValue = pos.x();
419	>	break;
420	>	case Token::wrappedY:
421	>	pos = sd->getPos();
422	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
423	>	propertyValue = pos.y();
424	>	break;
425	>	case Token::wrappedZ:
426	>	pos = sd->getPos();
427	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
428	>	propertyValue = pos.z();
429	>	break;
430	>	case Token::r:
431	>	propertyValue = sd->getPos().length();
432	>	break;
433	>	default:
434	>	unrecognizedAtomProperty(property);
435	>	}
436	>
437	>	bool match = false;
438	>	switch (comparator) {
439	>	case Token::opLT:
440	>	match = propertyValue < comparisonValue;
441	>	break;
442	>	case Token::opLE:
443	>	match = propertyValue <= comparisonValue;
444	>	break;
445	>	case Token::opGE:
446	>	match = propertyValue >= comparisonValue;
447	>	break;
448	>	case Token::opGT:
449	>	match = propertyValue > comparisonValue;
450	>	break;
451	>	case Token::opEQ:
452	>	match = propertyValue == comparisonValue;
453	>	break;
454	>	case Token::opNE:
455	>	match = propertyValue != comparisonValue;
456	>	break;
457	>	}
458	>
459	>	if (match)
460	>	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
461	>
462	>
463		}
464	+
465	+	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
466	+	int property, int comparator,
467	+	float comparisonValue) {
468	+	RealType propertyValue = 0.0;
469	+	Vector3d pos;
470	+
471	+	switch (property) {
472	+	case Token::mass:
473	+	propertyValue = mol->getMass();
474	+	break;
475	+	case Token::charge:
476	+	{
477	+	Molecule::AtomIterator ai;
478	+	Atom* atom;
479	+	for (atom = mol->beginAtom(ai); atom != NULL;
480	+	atom = mol->nextAtom(ai)) {
481	+	propertyValue+=  getCharge(atom);
482	+	}
483	+	}
484	+	break;
485	+	case Token::x:
486	+	propertyValue = mol->getCom().x();
487	+	break;
488	+	case Token::y:
489	+	propertyValue = mol->getCom().y();
490	+	break;
491	+	case Token::z:
492	+	propertyValue = mol->getCom().z();
493	+	break;
494	+	case Token::wrappedX:
495	+	pos = mol->getCom();
496	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
497	+	propertyValue = pos.x();
498	+	break;
499	+	case Token::wrappedY:
500	+	pos = mol->getCom();
501	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
502	+	propertyValue = pos.y();
503	+	break;
504	+	case Token::wrappedZ:
505	+	pos = mol->getCom();
506	+	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
507	+	propertyValue = pos.z();
508	+	break;
509	+	case Token::r:
510	+	propertyValue = mol->getCom().length();
511	+	break;
512	+	default:
513	+	unrecognizedMoleculeProperty(property);
514	+	}
515	+
516	+	bool match = false;
517	+	switch (comparator) {
518	+	case Token::opLT:
519	+	match = propertyValue < comparisonValue;
520	+	break;
521	+	case Token::opLE:
522	+	match = propertyValue <= comparisonValue;
523	+	break;
524	+	case Token::opGE:
525	+	match = propertyValue >= comparisonValue;
526	+	break;
527	+	case Token::opGT:
528	+	match = propertyValue > comparisonValue;
529	+	break;
530	+	case Token::opEQ:
531	+	match = propertyValue == comparisonValue;
532	+	break;
533	+	case Token::opNE:
534	+	match = propertyValue != comparisonValue;
535	+	break;
536	+	}
537	+
538	+	if (match)
539	+	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
540	+	}
541	+
542	+	void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
543	+	int property, int comparator,
544	+	float comparisonValue, int frame) {
545	+	RealType propertyValue = 0.0;
546	+	Vector3d pos;
547	+	switch (property) {
548	+	case Token::mass:
549	+	propertyValue = mol->getMass();
550	+	break;
551	+	case Token::charge:
552	+	{
553	+	Molecule::AtomIterator ai;
554	+	Atom* atom;
555	+	for (atom = mol->beginAtom(ai); atom != NULL;
556	+	atom = mol->nextAtom(ai)) {
557	+	propertyValue+=  getCharge(atom,frame);
558	+	}
559	+	}
560	+	break;
561	+	case Token::x:
562	+	propertyValue = mol->getCom(frame).x();
563	+	break;
564	+	case Token::y:
565	+	propertyValue = mol->getCom(frame).y();
566	+	break;
567	+	case Token::z:
568	+	propertyValue = mol->getCom(frame).z();
569	+	break;
570	+	case Token::wrappedX:
571	+	pos = mol->getCom(frame);
572	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
573	+	propertyValue = pos.x();
574	+	break;
575	+	case Token::wrappedY:
576	+	pos = mol->getCom(frame);
577	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
578	+	propertyValue = pos.y();
579	+	break;
580	+	case Token::wrappedZ:
581	+	pos = mol->getCom(frame);
582	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
583	+	propertyValue = pos.z();
584	+	break;
585	+
586	+	case Token::r:
587	+	propertyValue = mol->getCom(frame).length();
588	+	break;
589	+	default:
590	+	unrecognizedMoleculeProperty(property);
591	+	}
592	+
593	+	bool match = false;
594	+	switch (comparator) {
595	+	case Token::opLT:
596	+	match = propertyValue < comparisonValue;
597	+	break;
598	+	case Token::opLE:
599	+	match = propertyValue <= comparisonValue;
600	+	break;
601	+	case Token::opGE:
602	+	match = propertyValue >= comparisonValue;
603	+	break;
604	+	case Token::opGT:
605	+	match = propertyValue > comparisonValue;
606	+	break;
607	+	case Token::opEQ:
608	+	match = propertyValue == comparisonValue;
609	+	break;
610	+	case Token::opNE:
611	+	match = propertyValue != comparisonValue;
612	+	break;
613	+	}
614	+	if (match)
615	+	bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
616	+
617	+
618	+	}
619	+	void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
620	+	int property, int comparator,
621	+	float comparisonValue, int frame) {
622	+	RealType propertyValue = 0.0;
623	+	Vector3d pos;
624	+	switch (property) {
625	+	case Token::mass:
626	+	propertyValue = sd->getMass();
627	+	break;
628	+	case Token::charge:
629	+	if (sd->isAtom()){
630	+	Atom* atom = static_cast<Atom*>(sd);
631	+	propertyValue = getCharge(atom,frame);
632	+	} else if (sd->isRigidBody()) {
633	+	RigidBody* rb = static_cast<RigidBody*>(sd);
634	+	RigidBody::AtomIterator ai;
635	+	Atom* atom;
636	+	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
637	+	propertyValue+=  getCharge(atom,frame);
638	+	}
639	+	}
640	+	break;
641	+	case Token::x:
642	+	propertyValue = sd->getPos(frame).x();
643	+	break;
644	+	case Token::y:
645	+	propertyValue = sd->getPos(frame).y();
646	+	break;
647	+	case Token::z:
648	+	propertyValue = sd->getPos(frame).z();
649	+	break;
650	+	case Token::wrappedX:
651	+	pos = sd->getPos(frame);
652	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
653	+	propertyValue = pos.x();
654	+	break;
655	+	case Token::wrappedY:
656	+	pos = sd->getPos(frame);
657	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
658	+	propertyValue = pos.y();
659	+	break;
660	+	case Token::wrappedZ:
661	+	pos = sd->getPos(frame);
662	+	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
663	+	propertyValue = pos.z();
664	+	break;
665	+
666	+	case Token::r:
667	+	propertyValue = sd->getPos(frame).length();
668	+	break;
669	+	default:
670	+	unrecognizedAtomProperty(property);
671	+	}
672	+
673	+	bool match = false;
674	+	switch (comparator) {
675	+	case Token::opLT:
676	+	match = propertyValue < comparisonValue;
677	+	break;
678	+	case Token::opLE:
679	+	match = propertyValue <= comparisonValue;
680	+	break;
681	+	case Token::opGE:
682	+	match = propertyValue >= comparisonValue;
683	+	break;
684	+	case Token::opGT:
685	+	match = propertyValue > comparisonValue;
686	+	break;
687	+	case Token::opEQ:
688	+	match = propertyValue == comparisonValue;
689	+	break;
690	+	case Token::opNE:
691	+	match = propertyValue != comparisonValue;
692	+	break;
693	+	}
694	+	if (match)
695	+	bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
696	+	}
697
698	<	}
698	>
699	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
700	>	SelectionSet& bs){
701	>
702	>	boost::any withinSpec = instruction.value;
703	>	float distance;
704	>	if (withinSpec.type() == typeid(float)){
705	>	distance = boost::any_cast<float>(withinSpec);
706	>	} else if (withinSpec.type() == typeid(int)) {
707	>	distance = boost::any_cast<int>(withinSpec);
708	>	} else {
709	>	evalError("casting error in withinInstruction");
710	>	bs.clearAll();
711	>	}
712	>
713	>	bs = distanceFinder.find(bs, distance);
714	>	}
715	>
716	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
717	>	SelectionSet& bs, int frame){
718	>
719	>	boost::any withinSpec = instruction.value;
720	>	float distance;
721	>	if (withinSpec.type() == typeid(float)){
722	>	distance = boost::any_cast<float>(withinSpec);
723	>	} else if (withinSpec.type() == typeid(int)) {
724	>	distance = boost::any_cast<int>(withinSpec);
725	>	} else {
726	>	evalError("casting error in withinInstruction");
727	>	bs.clearAll();
728	>	}
729	>
730	>	bs = distanceFinder.find(bs, distance, frame);
731	>	}
732	>
733	>	void SelectionEvaluator::define() {
734	>	assert(statement.size() >= 3);
735	>
736	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
737	>
738	>	variables.insert(VariablesType::value_type(variable,
739	>	expression(statement, 2)));
740	>	}
741	>
742	>
743	>	/** @todo */
744	>	void SelectionEvaluator::predefine(const std::string& script) {
745	>
746	>	if (compiler.compile("#predefine", script)) {
747	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
748	>	if (aatoken.size() != 1) {
749	>	evalError("predefinition does not have exactly 1 command:"
750	>	+ script);
751	>	return;
752	>	}
753	>	std::vector<Token> statement = aatoken[0];
754	>	if (statement.size() > 2) {
755	>	int tok = statement[1].tok;
756	>	if (tok == Token::identifier ||
757	>	(tok & Token::predefinedset) == Token::predefinedset) {
758	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
759	>	variables.insert(VariablesType::value_type(variable, statement));
760	>
761	>	} else {
762	>	evalError("invalid variable name:" + script);
763	>	}
764	>	}else {
765	>	evalError("bad predefinition length:" + script);
766	>	}
767	>
768	>	} else {
769	>	evalError("predefined set compile error:" + script +
770	>	"\ncompile error:" + compiler.getErrorMessage());
771	>	}
772	>	}
773	>
774	>	void SelectionEvaluator::select(SelectionSet& bs){
775	>	bs = expression(statement, 1);
776	>	}
777	>
778	>	void SelectionEvaluator::select(SelectionSet& bs, int frame){
779	>	bs = expression(statement, 1, frame);
780	>	}
781	>
782	>	SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){
783	>
784	>	SelectionSet bs = createSelectionSets();
785	>	std::map<std::string, boost::any>::iterator i = variables.find(variable);
786	>
787	>	if (i != variables.end()) {
788	>	if (i->second.type() == typeid(SelectionSet)) {
789	>	return boost::any_cast<SelectionSet>(i->second);
790	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
791	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
792	>	i->second =  bs; /**@todo fixme */
793	>	return bs;
794	>	}
795	>	} else {
796	>	unrecognizedIdentifier(variable);
797	>	}
798	>
799	>	return bs;
800	>	}
801	>
802	>	SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){
803	>	return nameFinder.match(name);
804	>	}
805	>
806	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
807	>	std::vector<Token>::const_iterator i;
808	>	for (i = tokens.begin(); i != tokens.end(); ++i) {
809	>	if (i->tok & Token::dynamic) {
810	>	return true;
811	>	}
812	>	}
813	>
814	>	return false;
815	>	}
816	>
817	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
818	>	variables.clear();
819	>	//load predefine
820	>	//predefine();
821	>	}
822	>
823	>	SelectionSet SelectionEvaluator::createSelectionSets() {
824	>	SelectionSet ss(nObjects);
825	>	return ss;
826	>	}
827	>
828	>	SelectionSet SelectionEvaluator::evaluate() {
829	>	SelectionSet bs = createSelectionSets();
830	>	if (isLoaded_) {
831	>	pc = 0;
832	>	instructionDispatchLoop(bs);
833	>	}
834	>	return bs;
835	>	}
836	>
837	>	SelectionSet SelectionEvaluator::evaluate(int frame) {
838	>	SelectionSet bs = createSelectionSets();
839	>	if (isLoaded_) {
840	>	pc = 0;
841	>	instructionDispatchLoop(bs, frame);
842	>	}
843	>	return bs;
844	>	}
845	>
846	>	SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) {
847	>	SelectionSet bs = createSelectionSets();
848	>
849	>	if (value.type() == typeid(int)) {
850	>	int index = boost::any_cast<int>(value);
851	>	if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) {
852	>	invalidIndex(index);
853	>	} else {
854	>	bs = indexFinder.find(index);
855	>	}
856	>	} else if (value.type() == typeid(std::pair<int, int>)) {
857	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
858	>	assert(indexRange.first <= indexRange.second);
859	>	if (indexRange.first < 0 ||
860	>	indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) {
861	>	invalidIndexRange(indexRange);
862	>	}else {
863	>	bs = indexFinder.find(indexRange.first, indexRange.second);
864	>	}
865	>	}
866	>
867	>	return bs;
868	>	}
869	>
870	>	SelectionSet SelectionEvaluator::allInstruction() {
871	>	SelectionSet ss = createSelectionSets();
872	>
873	>	SimInfo::MoleculeIterator mi;
874	>	Molecule::AtomIterator ai;
875	>	Molecule::RigidBodyIterator rbIter;
876	>	Molecule::BondIterator bondIter;
877	>	Molecule::BendIterator bendIter;
878	>	Molecule::TorsionIterator torsionIter;
879	>	Molecule::InversionIterator inversionIter;
880	>
881	>	Molecule* mol;
882	>	Atom* atom;
883	>	RigidBody* rb;
884	>	Bond* bond;
885	>	Bend* bend;
886	>	Torsion* torsion;
887	>	Inversion* inversion;
888	>
889	>	// Doing the loop insures that we're actually on this processor.
890	>
891	>	for (mol = info->beginMolecule(mi); mol != NULL;
892	>	mol = info->nextMolecule(mi)) {
893	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
894	>	ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
895	>	}
896	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
897	>	rb = mol->nextRigidBody(rbIter)) {
898	>	ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
899	>	}
900	>	for (bond = mol->beginBond(bondIter); bond != NULL;
901	>	bond = mol->nextBond(bondIter)) {
902	>	ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
903	>	}
904	>	for (bend = mol->beginBend(bendIter); bend != NULL;
905	>	bend = mol->nextBend(bendIter)) {
906	>	ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
907	>	}
908	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
909	>	torsion = mol->nextTorsion(torsionIter)) {
910	>	ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
911	>	}
912	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
913	>	inversion = mol->nextInversion(inversionIter)) {
914	>	ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
915	>	}
916	>	ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
917	>	}
918	>
919	>	return ss;
920	>	}
921	>
922	>	SelectionSet SelectionEvaluator::hull() {
923	>	SelectionSet bs = createSelectionSets();
924	>
925	>	bs = hullFinder.findHull();
926	>	surfaceArea_ = hullFinder.getSurfaceArea();
927	>	hasSurfaceArea_ = true;
928	>	return bs;
929	>	}
930	>
931	>
932	>	SelectionSet SelectionEvaluator::hull(int frame) {
933	>	SelectionSet bs = createSelectionSets();
934	>
935	>	bs = hullFinder.findHull(frame);
936	>
937	>	return bs;
938	>	}
939	>
940	>	RealType SelectionEvaluator::getCharge(Atom* atom) {
941	>	RealType charge = 0.0;
942	>	AtomType* atomType = atom->getAtomType();
943	>
944	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
945	>	if ( fca.isFixedCharge() ) {
946	>	charge = fca.getCharge();
947	>	}
948	>
949	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
950	>	if ( fqa.isFluctuatingCharge() ) {
951	>	charge += atom->getFlucQPos();
952	>	}
953	>	return charge;
954	>	}
955	>
956	>	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
957	>	RealType charge = 0.0;
958	>	AtomType* atomType = atom->getAtomType();
959	>
960	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
961	>	if ( fca.isFixedCharge() ) {
962	>	charge = fca.getCharge();
963	>	}
964	>
965	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
966	>	if ( fqa.isFluctuatingCharge() ) {
967	>	charge += atom->getFlucQPos(frame);
968	>	}
969	>	return charge;
970	>	}
971	>
972	>	}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 281 by tim, Wed Feb 2 23:13:11 2005 UTC vs.
Revision 2071 by gezelter, Sat Mar 7 21:41:51 2015 UTC

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