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

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 278 by tim, Tue Feb 1 22:49:23 2005 UTC vs.
Revision 1903 by gezelter, Tue Jul 16 18:58:08 2013 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43	+	#include <stack>
44		#include "selection/SelectionEvaluator.hpp"
45	<	namespace oopse {
45	>	#include "primitives/Atom.hpp"
46	>	#include "primitives/DirectionalAtom.hpp"
47	>	#include "primitives/RigidBody.hpp"
48	>	#include "primitives/Molecule.hpp"
49	>	#include "io/ifstrstream.hpp"
50	>	#include "types/FixedChargeAdapter.hpp"
51	>	#include "types/FluctuatingChargeAdapter.hpp"
52
53
54	<	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	>	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() {
63	<	for (int i = scriptLevelMax; --i >= 0; )
64	<	stack[i] = null;
65	<	scriptLevel = 0;
100	>	void SelectionEvaluator::clearState() {
101		error = false;
102	<	errorMessage = null;
103	<	}
102	>	errorMessage = "";
103	>	}
104
105	<	bool SelectionEvaluator::loadScriptString(const std::string& script) {
105	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
106		clearState();
107	<	return loadScript(null, script);
108	<	}
107	>	return loadScript("", script);
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	<
116	<	void SelectionEvaluator::instructionDispatchLoop(){
117	<
118	<	while ( pc < aatoken.length) {
84	<	statement = aatoken[pc++];
85	<	statementLength = statement.length;
86	<	Token token = statement[0];
87	<	switch (token.tok) {
88	<	case Token.define:
89	<	define();
90	<	break;
91	<	case Token.select:
92	<	select();
93	<	break;
94	<	default:
95	<	unrecognizedCommand(token);
96	<	return;
97	<	}
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	<
122	<	void SelectionEvaluator::predefine(String script) {
123	<	if (compiler.compile("#predefine", script)) {
124	<	Token [][] aatoken = compiler.getAatokenCompiled();
125	<	if (aatoken.length != 1) {
126	<	viewer.scriptStatus("predefinition does not have exactly 1 command:"
127	<	+ script);
128	<	return;
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		}
109	–	Token[] statement = aatoken[0];
110	–	if (statement.length > 2) {
111	–	int tok = statement[1].tok;
112	–	if (tok == Token.identifier ||
113	–	(tok & Token.predefinedset) == Token.predefinedset) {
114	–	String variable = (String)statement[1].value;
115	–	variables.put(variable, statement);
116	–	} else {
117	–	viewer.scriptStatus("invalid variable name:" + script);
118	–	}
119	–	} else {
120	–	viewer.scriptStatus("bad predefinition length:" + script);
121	–	}
122	–	} else {
123	–	viewer.scriptStatus("predefined set compile error:" + script +
124	–	"\ncompile error:" + compiler.getErrorMessage());
147		}
148	+
149		}
150
151	+	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs, int frame){
152	+
153	+	while ( pc < aatoken.size()) {
154	+	statement = aatoken[pc++];
155	+	statementLength = statement.size();
156	+	Token token = statement[0];
157	+	switch (token.tok) {
158	+	case Token::define:
159	+	define();
160	+	break;
161	+	case Token::select:
162	+	select(bs, frame);
163	+	break;
164	+	default:
165	+	unrecognizedCommand(token);
166	+	return;
167	+	}
168	+	}
169
170	+	}
171
172	<	BitSet SelectionEvaluator::expression(Token[] code, int pcStart) throws ScriptException {
173	<	int numberOfAtoms = viewer.getAtomCount();
174	<	BitSet bs;
175	<	BitSet[] stack = new BitSet[10];
176	<	int sp = 0;
177	<
136	<	for (int pc = pcStart; ; ++pc) {
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	<	if (logMessages)
139	<	viewer.scriptStatus("instruction=" + instruction);
179	>
180		switch (instruction.tok) {
181	<	case Token.expressionBegin:
181	>	case Token::expressionBegin:
182		break;
183	<	case Token.expressionEnd:
144	<	break expression_loop;
145	<	case Token.all:
146	<	bs = stack[sp++] = new BitSet(numberOfAtoms);
147	<	for (int i = numberOfAtoms; --i >= 0; )
148	<	bs.set(i);
183	>	case Token::expressionEnd:
184		break;
185	<	case Token.none:
186	<	stack[sp++] = new BitSet();
185	>	case Token::all:
186	>	bs = allInstruction();
187	>	stack.push(bs);
188		break;
189	<	case Token.opOr:
190	<	bs = stack[--sp];
191	<	stack[sp-1].or(bs);
189	>	case Token::none:
190	>	bs = OpenMDBitSet(nStuntDouble);
191	>	stack.push(bs);
192		break;
193	<	case Token.opAnd:
194	<	bs = stack[--sp];
195	<	stack[sp-1].and(bs);
193	>	case Token::opOr:
194	>	bs = stack.top();
195	>	stack.pop();
196	>	stack.top() |= bs;
197		break;
198	<	case Token.opNot:
199	<	bs = stack[sp - 1];
200	<	notSet(bs);
198	>	case Token::opAnd:
199	>	bs = stack.top();
200	>	stack.pop();
201	>	stack.top() &= bs;
202		break;
203	<	case Token.within:
204	<	bs = stack[sp - 1];
167	<	stack[sp - 1] = new BitSet();
168	<	withinInstruction(instruction, bs, stack[sp - 1]);
203	>	case Token::opNot:
204	>	stack.top().flip();
205		break;
206	<	case Token.selected:
207	<	stack[sp++] = copyBitSet(viewer.getSelectionSet());
206	>	case Token::within:
207	>	withinInstruction(instruction, stack.top());
208	>	break;
209	>	case Token::hull:
210	>	stack.push(hull());
211		break;
212	<	case Token.y:
213	<	case Token.amino:
214	<	case Token.backbone:
215	<	case Token.solvent:
216	<	case Token.identifier:
178	<	case Token.sidechain:
179	<	case Token.surface:
180	<	stack[sp++] = lookupIdentifierValue((String)instruction.value);
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.opLT:
219	<	case Token.opLE:
184	<	case Token.opGE:
185	<	case Token.opGT:
186	<	case Token.opEQ:
187	<	case Token.opNE:
188	<	bs = stack[sp++] = new BitSet();
189	<	comparatorInstruction(instruction, bs);
218	>	case Token::index:
219	>	stack.push(indexInstruction(instruction.value));
220		break;
221	+	case Token::identifier:
222	+	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
223	+	break;
224	+	case Token::opLT:
225	+	case Token::opLE:
226	+	case Token::opGE:
227	+	case Token::opGT:
228	+	case Token::opEQ:
229	+	case Token::opNE:
230	+	stack.push(comparatorInstruction(instruction));
231	+	break;
232		default:
233		unrecognizedExpression();
234		}
235		}
236	<	if (sp != 1)
236	>	if (stack.size() != 1)
237		evalError("atom expression compiler error - stack over/underflow");
238	<	return stack[0];
238	>
239	>	return stack.top();
240		}
241
242
243	+	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
244	+	int pcStart, int frame) {
245	+	OpenMDBitSet bs;
246	+	std::stack<OpenMDBitSet> stack;
247	+
248	+	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
249	+	Token instruction = code[pc];
250
251	<	void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
252	<	int comparator = instruction.tok;
204	<	int property = instruction.intValue;
205	<	float propertyValue = 0; // just for temperature
206	<	int comparisonValue = ((Integer)instruction.value).intValue();
207	<	int numberOfAtoms = viewer.getAtomCount();
208	<	Frame frame = viewer.getFrame();
209	<	for (int i = 0; i < numberOfAtoms; ++i) {
210	<	Atom atom = frame.getAtomAt(i);
211	<	switch (property) {
212	<	case Token.atomno:
213	<	propertyValue = atom.getAtomNumber();
251	>	switch (instruction.tok) {
252	>	case Token::expressionBegin:
253		break;
254	<	case Token.elemno:
216	<	propertyValue = atom.getElementNumber();
254	>	case Token::expressionEnd:
255		break;
256	<	case Token.temperature:
257	<	propertyValue = atom.getBfactor100();
258	<	if (propertyValue < 0)
221	<	continue;
222	<	propertyValue /= 100;
223	<	break;
224	<	case Token._atomID:
225	<	propertyValue = atom.getSpecialAtomID();
226	<	if (propertyValue < 0)
227	<	continue;
256	>	case Token::all:
257	>	bs = allInstruction();
258	>	stack.push(bs);
259		break;
260	<	case Token._structure:
261	<	propertyValue = getProteinStructureType(atom);
262	<	if (propertyValue == -1)
232	<	continue;
260	>	case Token::none:
261	>	bs = OpenMDBitSet(nStuntDouble);
262	>	stack.push(bs);
263		break;
264	<	case Token.radius:
265	<	propertyValue = atom.getRasMolRadius();
264	>	case Token::opOr:
265	>	bs = stack.top();
266	>	stack.pop();
267	>	stack.top() |= bs;
268		break;
269	<	case Token._bondedcount:
270	<	propertyValue = atom.getCovalentBondCount();
269	>	case Token::opAnd:
270	>	bs = stack.top();
271	>	stack.pop();
272	>	stack.top() &= bs;
273		break;
274	<	case Token.model:
275	<	propertyValue = atom.getModelTagNumber();
274	>	case Token::opNot:
275	>	stack.top().flip();
276		break;
277	<	default:
278	<	unrecognizedAtomProperty(property);
245	<	}
246	<	boolean match = false;
247	<	switch (comparator) {
248	<	case Token.opLT:
249	<	match = propertyValue < comparisonValue;
277	>	case Token::within:
278	>	withinInstruction(instruction, stack.top(), frame);
279		break;
280	<	case Token.opLE:
281	<	match = propertyValue <= comparisonValue;
280	>	case Token::hull:
281	>	stack.push(hull(frame));
282		break;
283	<	case Token.opGE:
284	<	match = propertyValue >= comparisonValue;
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.opGT:
290	<	match = propertyValue > comparisonValue;
289	>	case Token::index:
290	>	stack.push(indexInstruction(instruction.value));
291		break;
292	<	case Token.opEQ:
293	<	match = propertyValue == comparisonValue;
292	>	case Token::identifier:
293	>	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
294		break;
295	<	case Token.opNE:
296	<	match = propertyValue != comparisonValue;
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		}
267	–	if (match)
268	–	bs.set(i);
306		}
307	+	if (stack.size() != 1)
308	+	evalError("atom expression compiler error - stack over/underflow");
309	+
310	+	return stack.top();
311		}
312
272	–	void SelectionEvaluator::withinInstruction(Token instruction, BitSet bs, BitSet bsResult)
313
274	–	Object withinSpec = instruction.value;
275	–	if (withinSpec instanceof Float) {
276	–	withinDistance(((Float)withinSpec).floatValue(), bs, bsResult);
277	–	return;
278	–	}
279	–	evalError("Unrecognized within parameter:" + withinSpec);
280	–	}
314
315	<	void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) {
316	<	Frame frame = viewer.getFrame();
317	<	for (int i = frame.getAtomCount(); --i >= 0; ) {
318	<	if (bs.get(i)) {
319	<	Atom atom = frame.getAtomAt(i);
320	<	AtomIterator iterWithin =
321	<	frame.getWithinIterator(atom, distance);
322	<	while (iterWithin.hasNext())
323	<	bsResult.set(iterWithin.next().getAtomIndex());
315	>	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
316	>	int comparator = instruction.tok;
317	>	int property = instruction.intValue;
318	>	float comparisonValue = boost::any_cast<float>(instruction.value);
319	>	OpenMDBitSet bs(nStuntDouble);
320	>	bs.clearAll();
321	>
322	>	SimInfo::MoleculeIterator mi;
323	>	Molecule* mol;
324	>	Molecule::AtomIterator ai;
325	>	Atom* atom;
326	>	Molecule::RigidBodyIterator rbIter;
327	>	RigidBody* rb;
328	>
329	>	for (mol = info->beginMolecule(mi); mol != NULL;
330	>	mol = info->nextMolecule(mi)) {
331	>
332	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
333	>	compareProperty(atom, bs, property, comparator, comparisonValue);
334		}
335	+
336	+	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
337	+	rb = mol->nextRigidBody(rbIter)) {
338	+	compareProperty(rb, bs, property, comparator, comparisonValue);
339	+	}
340		}
293	–	}
341
342	<	void SelectionEvaluator::define() throws ScriptException {
296	<	String variable = (String)statement[1].value;
297	<	variables.put(variable, (expression(statement, 2)));
342	>	return bs;
343		}
299	–	}
344
345	<	void SelectionEvaluator::predefine(Token[] statement) {
346	<	String variable = (String)statement[1].value;
347	<	variables.put(variable, statement);
345	>	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) {
346	>	int comparator = instruction.tok;
347	>	int property = instruction.intValue;
348	>	float comparisonValue = boost::any_cast<float>(instruction.value);
349	>	OpenMDBitSet bs(nStuntDouble);
350	>	bs.clearAll();
351	>
352	>	SimInfo::MoleculeIterator mi;
353	>	Molecule* mol;
354	>	Molecule::AtomIterator ai;
355	>	Atom* atom;
356	>	Molecule::RigidBodyIterator rbIter;
357	>	RigidBody* rb;
358	>
359	>	for (mol = info->beginMolecule(mi); mol != NULL;
360	>	mol = info->nextMolecule(mi)) {
361	>
362	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
363	>	compareProperty(atom, bs, property, comparator, comparisonValue, frame);
364	>	}
365	>
366	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
367	>	rb = mol->nextRigidBody(rbIter)) {
368	>	compareProperty(rb, bs, property, comparator, comparisonValue, frame);
369	>	}
370	>	}
371	>
372	>	return bs;
373		}
374
375	<	void SelectionEvaluator::select(){
376	<	// NOTE this is called by restrict()
377	<	if (statementLength == 1) {
378	<	viewer.selectAll();
379	<	if (!viewer.getRasmolHydrogenSetting())
380	<	viewer.excludeSelectionSet(getHydrogenSet());
381	<	if (!viewer.getRasmolHeteroSetting())
382	<	viewer.excludeSelectionSet(getHeteroSet());
375	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
376	>	int property, int comparator,
377	>	float comparisonValue) {
378	>	RealType propertyValue = 0.0;
379	>	Vector3d pos;
380	>	switch (property) {
381	>	case Token::mass:
382	>	propertyValue = sd->getMass();
383	>	break;
384	>	case Token::charge:
385	>	if (sd->isAtom()){
386	>	Atom* atom = static_cast<Atom*>(sd);
387	>	propertyValue = getCharge(atom);
388	>	} else if (sd->isRigidBody()) {
389	>	RigidBody* rb = static_cast<RigidBody*>(sd);
390	>	RigidBody::AtomIterator ai;
391	>	Atom* atom;
392	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
393	>	propertyValue+=  getCharge(atom);
394	>	}
395	>	}
396	>	break;
397	>	case Token::x:
398	>	propertyValue = sd->getPos().x();
399	>	break;
400	>	case Token::y:
401	>	propertyValue = sd->getPos().y();
402	>	break;
403	>	case Token::z:
404	>	propertyValue = sd->getPos().z();
405	>	break;
406	>	case Token::wrappedX:
407	>	pos = sd->getPos();
408	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
409	>	propertyValue = pos.x();
410	>	break;
411	>	case Token::wrappedY:
412	>	pos = sd->getPos();
413	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
414	>	propertyValue = pos.y();
415	>	break;
416	>	case Token::wrappedZ:
417	>	pos = sd->getPos();
418	>	info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
419	>	propertyValue = pos.z();
420	>	break;
421	>	case Token::r:
422	>	propertyValue = sd->getPos().length();
423	>	break;
424	>	default:
425	>	unrecognizedAtomProperty(property);
426	>	}
427	>
428	>	bool match = false;
429	>	switch (comparator) {
430	>	case Token::opLT:
431	>	match = propertyValue < comparisonValue;
432	>	break;
433	>	case Token::opLE:
434	>	match = propertyValue <= comparisonValue;
435	>	break;
436	>	case Token::opGE:
437	>	match = propertyValue >= comparisonValue;
438	>	break;
439	>	case Token::opGT:
440	>	match = propertyValue > comparisonValue;
441	>	break;
442	>	case Token::opEQ:
443	>	match = propertyValue == comparisonValue;
444	>	break;
445	>	case Token::opNE:
446	>	match = propertyValue != comparisonValue;
447	>	break;
448	>	}
449	>	if (match)
450	>	bs.setBitOn(sd->getGlobalIndex());
451	>
452	>
453	>	}
454	>
455	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
456	>	int property, int comparator,
457	>	float comparisonValue, int frame) {
458	>	RealType propertyValue = 0.0;
459	>	Vector3d pos;
460	>	switch (property) {
461	>	case Token::mass:
462	>	propertyValue = sd->getMass();
463	>	break;
464	>	case Token::charge:
465	>	if (sd->isAtom()){
466	>	Atom* atom = static_cast<Atom*>(sd);
467	>	propertyValue = getCharge(atom,frame);
468	>	} else if (sd->isRigidBody()) {
469	>	RigidBody* rb = static_cast<RigidBody*>(sd);
470	>	RigidBody::AtomIterator ai;
471	>	Atom* atom;
472	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
473	>	propertyValue+=  getCharge(atom,frame);
474	>	}
475	>	}
476	>	break;
477	>	case Token::x:
478	>	propertyValue = sd->getPos(frame).x();
479	>	break;
480	>	case Token::y:
481	>	propertyValue = sd->getPos(frame).y();
482	>	break;
483	>	case Token::z:
484	>	propertyValue = sd->getPos(frame).z();
485	>	break;
486	>	case Token::wrappedX:
487	>	pos = sd->getPos(frame);
488	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
489	>	propertyValue = pos.x();
490	>	break;
491	>	case Token::wrappedY:
492	>	pos = sd->getPos(frame);
493	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
494	>	propertyValue = pos.y();
495	>	break;
496	>	case Token::wrappedZ:
497	>	pos = sd->getPos(frame);
498	>	info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
499	>	propertyValue = pos.z();
500	>	break;
501	>
502	>	case Token::r:
503	>	propertyValue = sd->getPos(frame).length();
504	>	break;
505	>	default:
506	>	unrecognizedAtomProperty(property);
507	>	}
508	>
509	>	bool match = false;
510	>	switch (comparator) {
511	>	case Token::opLT:
512	>	match = propertyValue < comparisonValue;
513	>	break;
514	>	case Token::opLE:
515	>	match = propertyValue <= comparisonValue;
516	>	break;
517	>	case Token::opGE:
518	>	match = propertyValue >= comparisonValue;
519	>	break;
520	>	case Token::opGT:
521	>	match = propertyValue > comparisonValue;
522	>	break;
523	>	case Token::opEQ:
524	>	match = propertyValue == comparisonValue;
525	>	break;
526	>	case Token::opNE:
527	>	match = propertyValue != comparisonValue;
528	>	break;
529	>	}
530	>	if (match)
531	>	bs.setBitOn(sd->getGlobalIndex());
532	>
533	>
534	>	}
535	>
536	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
537	>	OpenMDBitSet& bs){
538	>
539	>	boost::any withinSpec = instruction.value;
540	>	float distance;
541	>	if (withinSpec.type() == typeid(float)){
542	>	distance = boost::any_cast<float>(withinSpec);
543	>	} else if (withinSpec.type() == typeid(int)) {
544	>	distance = boost::any_cast<int>(withinSpec);
545		} else {
546	<	viewer.setSelectionSet(expression(statement, 1));
546	>	evalError("casting error in withinInstruction");
547	>	bs.clearAll();
548		}
549	<	viewer.scriptStatus("" + viewer.getSelectionCount() + " atoms selected");
549	>
550	>	bs = distanceFinder.find(bs, distance);
551		}
552	+
553	+	void SelectionEvaluator::withinInstruction(const Token& instruction,
554	+	OpenMDBitSet& bs, int frame){
555	+
556	+	boost::any withinSpec = instruction.value;
557	+	float distance;
558	+	if (withinSpec.type() == typeid(float)){
559	+	distance = boost::any_cast<float>(withinSpec);
560	+	} else if (withinSpec.type() == typeid(int)) {
561	+	distance = boost::any_cast<int>(withinSpec);
562	+	} else {
563	+	evalError("casting error in withinInstruction");
564	+	bs.clearAll();
565	+	}
566	+
567	+	bs = distanceFinder.find(bs, distance, frame);
568	+	}
569
570	<	}
570	>	void SelectionEvaluator::define() {
571	>	assert(statement.size() >= 3);
572	>
573	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
574	>
575	>	variables.insert(VariablesType::value_type(variable,
576	>	expression(statement, 2)));
577	>	}
578	>
579	>
580	>	/** @todo */
581	>	void SelectionEvaluator::predefine(const std::string& script) {
582	>
583	>	if (compiler.compile("#predefine", script)) {
584	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
585	>	if (aatoken.size() != 1) {
586	>	evalError("predefinition does not have exactly 1 command:"
587	>	+ script);
588	>	return;
589	>	}
590	>	std::vector<Token> statement = aatoken[0];
591	>	if (statement.size() > 2) {
592	>	int tok = statement[1].tok;
593	>	if (tok == Token::identifier ||
594	>	(tok & Token::predefinedset) == Token::predefinedset) {
595	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
596	>	variables.insert(VariablesType::value_type(variable, statement));
597	>
598	>	} else {
599	>	evalError("invalid variable name:" + script);
600	>	}
601	>	}else {
602	>	evalError("bad predefinition length:" + script);
603	>	}
604	>
605	>	} else {
606	>	evalError("predefined set compile error:" + script +
607	>	"\ncompile error:" + compiler.getErrorMessage());
608	>	}
609	>	}
610	>
611	>	void SelectionEvaluator::select(OpenMDBitSet& bs){
612	>	bs = expression(statement, 1);
613	>	}
614	>
615	>	void SelectionEvaluator::select(OpenMDBitSet& bs, int frame){
616	>	bs = expression(statement, 1, frame);
617	>	}
618	>
619	>	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
620	>
621	>	OpenMDBitSet bs(nStuntDouble);
622	>	std::map<std::string, boost::any>::iterator i = variables.find(variable);
623	>
624	>	if (i != variables.end()) {
625	>	if (i->second.type() == typeid(OpenMDBitSet)) {
626	>	return boost::any_cast<OpenMDBitSet>(i->second);
627	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
628	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
629	>	i->second =  bs; /**@todo fixme */
630	>	return bs;
631	>	}
632	>	} else {
633	>	unrecognizedIdentifier(variable);
634	>	}
635	>
636	>	return bs;
637	>	}
638	>
639	>	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
640	>	return nameFinder.match(name);
641	>	}
642	>
643	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
644	>	std::vector<Token>::const_iterator i;
645	>	for (i = tokens.begin(); i != tokens.end(); ++i) {
646	>	if (i->tok & Token::dynamic) {
647	>	return true;
648	>	}
649	>	}
650	>
651	>	return false;
652	>	}
653	>
654	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
655	>	variables.clear();
656	>	//load predefine
657	>	//predefine();
658	>	}
659	>
660	>	OpenMDBitSet SelectionEvaluator::evaluate() {
661	>	OpenMDBitSet bs(nStuntDouble);
662	>	if (isLoaded_) {
663	>	pc = 0;
664	>	instructionDispatchLoop(bs);
665	>	}
666	>	return bs;
667	>	}
668	>
669	>	OpenMDBitSet SelectionEvaluator::evaluate(int frame) {
670	>	OpenMDBitSet bs(nStuntDouble);
671	>	if (isLoaded_) {
672	>	pc = 0;
673	>	instructionDispatchLoop(bs, frame);
674	>	}
675	>	return bs;
676	>	}
677	>
678	>	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
679	>	OpenMDBitSet bs(nStuntDouble);
680	>
681	>	if (value.type() == typeid(int)) {
682	>	int index = boost::any_cast<int>(value);
683	>	if (index < 0 || index >= bs.size()) {
684	>	invalidIndex(index);
685	>	} else {
686	>	bs = indexFinder.find(index);
687	>	}
688	>	} else if (value.type() == typeid(std::pair<int, int>)) {
689	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
690	>	assert(indexRange.first <= indexRange.second);
691	>	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
692	>	invalidIndexRange(indexRange);
693	>	}else {
694	>	bs = indexFinder.find(indexRange.first, indexRange.second);
695	>	}
696	>	}
697	>
698	>	return bs;
699	>	}
700	>
701	>	OpenMDBitSet SelectionEvaluator::allInstruction() {
702	>	OpenMDBitSet bs(nStuntDouble);
703	>
704	>	SimInfo::MoleculeIterator mi;
705	>	Molecule* mol;
706	>	Molecule::AtomIterator ai;
707	>	Atom* atom;
708	>	Molecule::RigidBodyIterator rbIter;
709	>	RigidBody* rb;
710	>
711	>	// Doing the loop insures that we're actually on this processor.
712	>
713	>	for (mol = info->beginMolecule(mi); mol != NULL;
714	>	mol = info->nextMolecule(mi)) {
715	>
716	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
717	>	bs.setBitOn(atom->getGlobalIndex());
718	>	}
719	>
720	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
721	>	rb = mol->nextRigidBody(rbIter)) {
722	>	bs.setBitOn(rb->getGlobalIndex());
723	>	}
724	>	}
725	>
726	>	return bs;
727	>	}
728	>
729	>	OpenMDBitSet SelectionEvaluator::hull() {
730	>	OpenMDBitSet bs(nStuntDouble);
731	>
732	>	bs = hullFinder.findHull();
733	>	surfaceArea_ = hullFinder.getSurfaceArea();
734	>	hasSurfaceArea_ = true;
735	>	return bs;
736	>	}
737	>
738	>
739	>	OpenMDBitSet SelectionEvaluator::hull(int frame) {
740	>	OpenMDBitSet bs(nStuntDouble);
741	>
742	>	bs = hullFinder.findHull(frame);
743	>
744	>	return bs;
745	>	}
746	>
747	>	RealType SelectionEvaluator::getCharge(Atom* atom) {
748	>	RealType charge = 0.0;
749	>	AtomType* atomType = atom->getAtomType();
750	>
751	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
752	>	if ( fca.isFixedCharge() ) {
753	>	charge = fca.getCharge();
754	>	}
755	>
756	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
757	>	if ( fqa.isFluctuatingCharge() ) {
758	>	charge += atom->getFlucQPos();
759	>	}
760	>	return charge;
761	>	}
762	>
763	>	RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
764	>	RealType charge = 0.0;
765	>	AtomType* atomType = atom->getAtomType();
766	>
767	>	FixedChargeAdapter fca = FixedChargeAdapter(atomType);
768	>	if ( fca.isFixedCharge() ) {
769	>	charge = fca.getCharge();
770	>	}
771	>
772	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
773	>	if ( fqa.isFluctuatingCharge() ) {
774	>	charge += atom->getFlucQPos(frame);
775	>	}
776	>	return charge;
777	>	}
778	>
779	>	}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 278 by tim, Tue Feb 1 22:49:23 2005 UTC vs.
Revision 1903 by gezelter, Tue Jul 16 18:58:08 2013 UTC

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