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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 1801 by gezelter, Mon Oct 1 18:21:15 2012 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, 24107 (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
51	+	namespace OpenMD {
52
53	<	bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
53	>
54	>	SelectionEvaluator::SelectionEvaluator(SimInfo* si)
55	>	: info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
56	>	indexFinder(info),
57	>	isLoaded_(false){
58	>	nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
59	>	}
60	>
61	>	bool SelectionEvaluator::loadScript(const std::string& filename,
62	>	const std::string& script) {
63	>	clearDefinitionsAndLoadPredefined();
64		this->filename = filename;
65		this->script = script;
66		if (! compiler.compile(filename, script)) {
67	<	error = true;
68	<	errorMessage = compiler.getErrorMessage();
69	<	return false;
67	>	error = true;
68	>	errorMessage = compiler.getErrorMessage();
69	>
70	>	sprintf( painCave.errMsg,
71	>	"SelectionCompiler Error: %s\n", errorMessage.c_str());
72	>	painCave.severity = OPENMD_ERROR;
73	>	painCave.isFatal = 1;
74	>	simError();
75	>	return false;
76		}
77
78		pc = 0;
79		aatoken = compiler.getAatokenCompiled();
80		linenumbers = compiler.getLineNumbers();
81		lineIndices = compiler.getLineIndices();
82	+
83	+	std::vector<std::vector<Token> >::const_iterator i;
84	+
85	+	isDynamic_ = false;
86	+	for (i = aatoken.begin(); i != aatoken.end(); ++i) {
87	+	if (containDynamicToken(*i)) {
88	+	isDynamic_ = true;
89	+	break;
90	+	}
91	+	}
92	+
93	+	isLoaded_ = true;
94		return true;
95	<	}
95	>	}
96
97	<	void SelectionEvaluator::clearState() {
63	<	for (int i = scriptLevelMax; --i >= 0; )
64	<	stack[i] = null;
65	<	scriptLevel = 0;
97	>	void SelectionEvaluator::clearState() {
98		error = false;
99	<	errorMessage = null;
100	<	}
99	>	errorMessage = "";
100	>	}
101
102	<	bool SelectionEvaluator::loadScriptString(const std::string& script) {
102	>	bool SelectionEvaluator::loadScriptString(const std::string& script) {
103		clearState();
104	<	return loadScript(null, script);
105	<	}
104	>	return loadScript("", script);
105	>	}
106
107	<	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
107	>	bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
108		clearState();
109		return loadScriptFileInternal(filename);
110	<	}
110	>	}
111
112	<
113	<	void SelectionEvaluator::instructionDispatchLoop(){
114	<
115	<	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	<	}
112	>	bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
113	>	ifstrstream ifs(filename.c_str());
114	>	if (!ifs.is_open()) {
115	>	return false;
116		}
117	<	}
118	<
119	<	void SelectionEvaluator::predefine(String script) {
120	<	if (compiler.compile("#predefine", script)) {
121	<	Token [][] aatoken = compiler.getAatokenCompiled();
122	<	if (aatoken.length != 1) {
123	<	viewer.scriptStatus("predefinition does not have exactly 1 command:"
124	<	+ script);
125	<	return;
117	>
118	>	const int bufferSize = 65535;
119	>	char buffer[bufferSize];
120	>	std::string script;
121	>	while(ifs.getline(buffer, bufferSize)) {
122	>	script += buffer;
123	>	}
124	>	return loadScript(filename, script);
125	>	}
126	>
127	>	void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
128	>
129	>	while ( pc < aatoken.size()) {
130	>	statement = aatoken[pc++];
131	>	statementLength = statement.size();
132	>	Token token = statement[0];
133	>	switch (token.tok) {
134	>	case Token::define:
135	>	define();
136	>	break;
137	>	case Token::select:
138	>	select(bs);
139	>	break;
140	>	default:
141	>	unrecognizedCommand(token);
142	>	return;
143		}
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());
144		}
145	+
146		}
147
148	<
149	<
150	<	BitSet SelectionEvaluator::expression(Token[] code, int pcStart) throws ScriptException {
151	<	int numberOfAtoms = viewer.getAtomCount();
152	<	BitSet bs;
153	<	BitSet[] stack = new BitSet[10];
134	<	int sp = 0;
135	<
136	<	for (int pc = pcStart; ; ++pc) {
148	>	OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
149	>	int pcStart) {
150	>	OpenMDBitSet bs;
151	>	std::stack<OpenMDBitSet> stack;
152	>
153	>	for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
154		Token instruction = code[pc];
155	<	if (logMessages)
139	<	viewer.scriptStatus("instruction=" + instruction);
155	>
156		switch (instruction.tok) {
157	<	case Token.expressionBegin:
157	>	case Token::expressionBegin:
158		break;
159	<	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);
159	>	case Token::expressionEnd:
160		break;
161	<	case Token.none:
162	<	stack[sp++] = new BitSet();
161	>	case Token::all:
162	>	bs = allInstruction();
163	>	stack.push(bs);
164		break;
165	<	case Token.opOr:
166	<	bs = stack[--sp];
167	<	stack[sp-1].or(bs);
165	>	case Token::none:
166	>	bs = OpenMDBitSet(nStuntDouble);
167	>	stack.push(bs);
168		break;
169	<	case Token.opAnd:
170	<	bs = stack[--sp];
171	<	stack[sp-1].and(bs);
169	>	case Token::opOr:
170	>	bs = stack.top();
171	>	stack.pop();
172	>	stack.top() |= bs;
173		break;
174	<	case Token.opNot:
175	<	bs = stack[sp - 1];
176	<	notSet(bs);
174	>	case Token::opAnd:
175	>	bs = stack.top();
176	>	stack.pop();
177	>	stack.top() &= bs;
178		break;
179	<	case Token.within:
180	<	bs = stack[sp - 1];
167	<	stack[sp - 1] = new BitSet();
168	<	withinInstruction(instruction, bs, stack[sp - 1]);
179	>	case Token::opNot:
180	>	stack.top().flip();
181		break;
182	<	case Token.selected:
183	<	stack[sp++] = copyBitSet(viewer.getSelectionSet());
182	>	case Token::within:
183	>	withinInstruction(instruction, stack.top());
184		break;
185	<	case Token.y:
186	<	case Token.amino:
175	<	case Token.backbone:
176	<	case Token.solvent:
177	<	case Token.identifier:
178	<	case Token.sidechain:
179	<	case Token.surface:
180	<	stack[sp++] = lookupIdentifierValue((String)instruction.value);
185	>	case Token::hull:
186	>	stack.push(hull());
187		break;
188	<	case Token.opLT:
189	<	case Token.opLE:
190	<	case Token.opGE:
191	<	case Token.opGT:
192	<	case Token.opEQ:
187	<	case Token.opNE:
188	<	bs = stack[sp++] = new BitSet();
189	<	comparatorInstruction(instruction, bs);
188	>	//case Token::selected:
189	>	//  stack.push(getSelectionSet());
190	>	//  break;
191	>	case Token::name:
192	>	stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
193		break;
194	+	case Token::index:
195	+	stack.push(indexInstruction(instruction.value));
196	+	break;
197	+	case Token::identifier:
198	+	stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
199	+	break;
200	+	case Token::opLT:
201	+	case Token::opLE:
202	+	case Token::opGE:
203	+	case Token::opGT:
204	+	case Token::opEQ:
205	+	case Token::opNE:
206	+	stack.push(comparatorInstruction(instruction));
207	+	break;
208		default:
209		unrecognizedExpression();
210		}
211		}
212	<	if (sp != 1)
212	>	if (stack.size() != 1)
213		evalError("atom expression compiler error - stack over/underflow");
214	<	return stack[0];
214	>
215	>	return stack.top();
216		}
217
218
219
220	<	void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
220	>	OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
221		int comparator = instruction.tok;
222		int property = instruction.intValue;
223	<	float propertyValue = 0; // just for temperature
224	<	int comparisonValue = ((Integer)instruction.value).intValue();
225	<	int numberOfAtoms = viewer.getAtomCount();
226	<	Frame frame = viewer.getFrame();
227	<	for (int i = 0; i < numberOfAtoms; ++i) {
228	<	Atom atom = frame.getAtomAt(i);
229	<	switch (property) {
230	<	case Token.atomno:
231	<	propertyValue = atom.getAtomNumber();
232	<	break;
215	<	case Token.elemno:
216	<	propertyValue = atom.getElementNumber();
217	<	break;
218	<	case Token.temperature:
219	<	propertyValue = atom.getBfactor100();
220	<	if (propertyValue < 0)
221	<	continue;
222	<	propertyValue /= 100;
223	<	break;
224	<	case Token._atomID:
225	<	propertyValue = atom.getSpecialAtomID();
226	<	if (propertyValue < 0)
227	<	continue;
228	<	break;
229	<	case Token._structure:
230	<	propertyValue = getProteinStructureType(atom);
231	<	if (propertyValue == -1)
232	<	continue;
233	<	break;
234	<	case Token.radius:
235	<	propertyValue = atom.getRasMolRadius();
236	<	break;
237	<	case Token._bondedcount:
238	<	propertyValue = atom.getCovalentBondCount();
239	<	break;
240	<	case Token.model:
241	<	propertyValue = atom.getModelTagNumber();
242	<	break;
243	<	default:
244	<	unrecognizedAtomProperty(property);
245	<	}
246	<	boolean match = false;
247	<	switch (comparator) {
248	<	case Token.opLT:
249	<	match = propertyValue < comparisonValue;
250	<	break;
251	<	case Token.opLE:
252	<	match = propertyValue <= comparisonValue;
253	<	break;
254	<	case Token.opGE:
255	<	match = propertyValue >= comparisonValue;
256	<	break;
257	<	case Token.opGT:
258	<	match = propertyValue > comparisonValue;
259	<	break;
260	<	case Token.opEQ:
261	<	match = propertyValue == comparisonValue;
262	<	break;
263	<	case Token.opNE:
264	<	match = propertyValue != comparisonValue;
265	<	break;
266	<	}
267	<	if (match)
268	<	bs.set(i);
269	<	}
270	<	}
223	>	float comparisonValue = boost::any_cast<float>(instruction.value);
224	>	OpenMDBitSet bs(nStuntDouble);
225	>	bs.clearAll();
226	>
227	>	SimInfo::MoleculeIterator mi;
228	>	Molecule* mol;
229	>	Molecule::AtomIterator ai;
230	>	Atom* atom;
231	>	Molecule::RigidBodyIterator rbIter;
232	>	RigidBody* rb;
233
234	<	void SelectionEvaluator::withinInstruction(Token instruction, BitSet bs, BitSet bsResult)
234	>	for (mol = info->beginMolecule(mi); mol != NULL;
235	>	mol = info->nextMolecule(mi)) {
236
237	<	Object withinSpec = instruction.value;
238	<	if (withinSpec instanceof Float) {
239	<	withinDistance(((Float)withinSpec).floatValue(), bs, bsResult);
240	<	return;
237	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
238	>	compareProperty(atom, bs, property, comparator, comparisonValue);
239	>	}
240	>
241	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
242	>	rb = mol->nextRigidBody(rbIter)) {
243	>	compareProperty(rb, bs, property, comparator, comparisonValue);
244	>	}
245		}
279	–	evalError("Unrecognized within parameter:" + withinSpec);
280	–	}
246
247	<	void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) {
248	<	Frame frame = viewer.getFrame();
249	<	for (int i = frame.getAtomCount(); --i >= 0; ) {
250	<	if (bs.get(i)) {
251	<	Atom atom = frame.getAtomAt(i);
252	<	AtomIterator iterWithin =
253	<	frame.getWithinIterator(atom, distance);
254	<	while (iterWithin.hasNext())
255	<	bsResult.set(iterWithin.next().getAtomIndex());
247	>	return bs;
248	>	}
249	>
250	>	void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
251	>	int property, int comparator,
252	>	float comparisonValue) {
253	>	RealType propertyValue = 0.0;
254	>	switch (property) {
255	>	case Token::mass:
256	>	propertyValue = sd->getMass();
257	>	break;
258	>	case Token::charge:
259	>	if (sd->isAtom()){
260	>	Atom* atom = static_cast<Atom*>(sd);
261	>	propertyValue = getCharge(atom);
262	>	} else if (sd->isRigidBody()) {
263	>	RigidBody* rb = static_cast<RigidBody*>(sd);
264	>	RigidBody::AtomIterator ai;
265	>	Atom* atom;
266	>	for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
267	>	propertyValue+=  getCharge(atom);
268	>	}
269		}
270	+	break;
271	+	case Token::x:
272	+	propertyValue = sd->getPos().x();
273	+	break;
274	+	case Token::y:
275	+	propertyValue = sd->getPos().y();
276	+	break;
277	+	case Token::z:
278	+	propertyValue = sd->getPos().z();
279	+	break;
280	+	case Token::r:
281	+	propertyValue = sd->getPos().length();
282	+	break;
283	+	default:
284	+	unrecognizedAtomProperty(property);
285		}
286	+
287	+	bool match = false;
288	+	switch (comparator) {
289	+	case Token::opLT:
290	+	match = propertyValue < comparisonValue;
291	+	break;
292	+	case Token::opLE:
293	+	match = propertyValue <= comparisonValue;
294	+	break;
295	+	case Token::opGE:
296	+	match = propertyValue >= comparisonValue;
297	+	break;
298	+	case Token::opGT:
299	+	match = propertyValue > comparisonValue;
300	+	break;
301	+	case Token::opEQ:
302	+	match = propertyValue == comparisonValue;
303	+	break;
304	+	case Token::opNE:
305	+	match = propertyValue != comparisonValue;
306	+	break;
307	+	}
308	+	if (match)
309	+	bs.setBitOn(sd->getGlobalIndex());
310	+
311		}
312
313	<	void SelectionEvaluator::define() throws ScriptException {
314	<	String variable = (String)statement[1].value;
315	<	variables.put(variable, (expression(statement, 2)));
313	>	void SelectionEvaluator::withinInstruction(const Token& instruction,
314	>	OpenMDBitSet& bs){
315	>
316	>	boost::any withinSpec = instruction.value;
317	>	float distance;
318	>	if (withinSpec.type() == typeid(float)){
319	>	distance = boost::any_cast<float>(withinSpec);
320	>	} else if (withinSpec.type() == typeid(int)) {
321	>	distance = boost::any_cast<int>(withinSpec);
322	>	} else {
323	>	evalError("casting error in withinInstruction");
324	>	bs.clearAll();
325	>	}
326	>
327	>	bs = distanceFinder.find(bs, distance);
328		}
329	<	}
329	>
330	>	void SelectionEvaluator::define() {
331	>	assert(statement.size() >= 3);
332	>
333	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
334	>
335	>	variables.insert(VariablesType::value_type(variable,
336	>	expression(statement, 2)));
337	>	}
338	>
339
340	<	void SelectionEvaluator::predefine(Token[] statement) {
341	<	String variable = (String)statement[1].value;
342	<	variables.put(variable, statement);
340	>	/** @todo */
341	>	void SelectionEvaluator::predefine(const std::string& script) {
342	>
343	>	if (compiler.compile("#predefine", script)) {
344	>	std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
345	>	if (aatoken.size() != 1) {
346	>	evalError("predefinition does not have exactly 1 command:"
347	>	+ script);
348	>	return;
349	>	}
350	>	std::vector<Token> statement = aatoken[0];
351	>	if (statement.size() > 2) {
352	>	int tok = statement[1].tok;
353	>	if (tok == Token::identifier ||
354	>	(tok & Token::predefinedset) == Token::predefinedset) {
355	>	std::string variable = boost::any_cast<std::string>(statement[1].value);
356	>	variables.insert(VariablesType::value_type(variable, statement));
357	>
358	>	} else {
359	>	evalError("invalid variable name:" + script);
360	>	}
361	>	}else {
362	>	evalError("bad predefinition length:" + script);
363	>	}
364	>
365	>	} else {
366	>	evalError("predefined set compile error:" + script +
367	>	"\ncompile error:" + compiler.getErrorMessage());
368	>	}
369		}
370
371	<	void SelectionEvaluator::select(){
372	<	// NOTE this is called by restrict()
373	<	if (statementLength == 1) {
374	<	viewer.selectAll();
375	<	if (!viewer.getRasmolHydrogenSetting())
376	<	viewer.excludeSelectionSet(getHydrogenSet());
377	<	if (!viewer.getRasmolHeteroSetting())
378	<	viewer.excludeSelectionSet(getHeteroSet());
371	>	void SelectionEvaluator::select(OpenMDBitSet& bs){
372	>	bs = expression(statement, 1);
373	>	}
374	>
375	>	OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
376	>
377	>	OpenMDBitSet bs(nStuntDouble);
378	>	std::map<std::string, boost::any>::iterator i = variables.find(variable);
379	>
380	>	if (i != variables.end()) {
381	>	if (i->second.type() == typeid(OpenMDBitSet)) {
382	>	return boost::any_cast<OpenMDBitSet>(i->second);
383	>	} else if (i->second.type() ==  typeid(std::vector<Token>)){
384	>	bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
385	>	i->second =  bs; /**@todo fixme */
386	>	return bs;
387	>	}
388		} else {
389	<	viewer.setSelectionSet(expression(statement, 1));
389	>	unrecognizedIdentifier(variable);
390		}
391	<	viewer.scriptStatus("" + viewer.getSelectionCount() + " atoms selected");
391	>
392	>	return bs;
393		}
394
395	<	}
395	>	OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){
396	>	return nameFinder.match(name);
397	>	}
398	>
399	>	bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
400	>	std::vector<Token>::const_iterator i;
401	>	for (i = tokens.begin(); i != tokens.end(); ++i) {
402	>	if (i->tok & Token::dynamic) {
403	>	return true;
404	>	}
405	>	}
406	>
407	>	return false;
408	>	}
409	>
410	>	void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
411	>	variables.clear();
412	>	//load predefine
413	>	//predefine();
414	>	}
415	>
416	>	OpenMDBitSet SelectionEvaluator::evaluate() {
417	>	OpenMDBitSet bs(nStuntDouble);
418	>	if (isLoaded_) {
419	>	pc = 0;
420	>	instructionDispatchLoop(bs);
421	>	}
422	>
423	>	return bs;
424	>	}
425	>
426	>	OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
427	>	OpenMDBitSet bs(nStuntDouble);
428	>
429	>	if (value.type() == typeid(int)) {
430	>	int index = boost::any_cast<int>(value);
431	>	if (index < 0 || index >= bs.size()) {
432	>	invalidIndex(index);
433	>	} else {
434	>	bs = indexFinder.find(index);
435	>	}
436	>	} else if (value.type() == typeid(std::pair<int, int>)) {
437	>	std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
438	>	assert(indexRange.first <= indexRange.second);
439	>	if (indexRange.first < 0 || indexRange.second >= bs.size()) {
440	>	invalidIndexRange(indexRange);
441	>	}else {
442	>	bs = indexFinder.find(indexRange.first, indexRange.second);
443	>	}
444	>	}
445	>
446	>	return bs;
447	>	}
448	>
449	>	OpenMDBitSet SelectionEvaluator::allInstruction() {
450	>	OpenMDBitSet bs(nStuntDouble);
451	>
452	>	SimInfo::MoleculeIterator mi;
453	>	Molecule* mol;
454	>	Molecule::AtomIterator ai;
455	>	Atom* atom;
456	>	Molecule::RigidBodyIterator rbIter;
457	>	RigidBody* rb;
458	>
459	>	// Doing the loop insures that we're actually on this processor.
460	>
461	>	for (mol = info->beginMolecule(mi); mol != NULL;
462	>	mol = info->nextMolecule(mi)) {
463	>
464	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
465	>	bs.setBitOn(atom->getGlobalIndex());
466	>	}
467	>
468	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
469	>	rb = mol->nextRigidBody(rbIter)) {
470	>	bs.setBitOn(rb->getGlobalIndex());
471	>	}
472	>	}
473	>
474	>	return bs;
475	>	}
476	>
477	>	OpenMDBitSet SelectionEvaluator::hull() {
478	>	OpenMDBitSet bs(nStuntDouble);
479	>
480	>	bs = hullFinder.findHull();
481	>
482	>	return bs;
483	>	}
484	>
485	>	RealType SelectionEvaluator::getCharge(Atom* atom) {
486	>	RealType charge =0.0;
487	>	AtomType* atomType = atom->getAtomType();
488	>	if (atomType->isCharge()) {
489	>	GenericData* data = atomType->getPropertyByName("Charge");
490	>	if (data != NULL) {
491	>	DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
492	>
493	>	if (doubleData != NULL) {
494	>	charge = doubleData->getData();
495	>
496	>	} else {
497	>	sprintf( painCave.errMsg,
498	>	"Can not cast GenericData to DoubleGenericData\n");
499	>	painCave.severity = OPENMD_ERROR;
500	>	painCave.isFatal = 1;
501	>	simError();
502	>	}
503	>	}
504	>	}
505	>
506	>	return charge;
507	>	}
508	>
509	>	}

Comparing trunk/src/selection/SelectionEvaluator.cpp (property svn:keywords):
Revision 278 by tim, Tue Feb 1 22:49:23 2005 UTC vs.
Revision 1801 by gezelter, Mon Oct 1 18:21:15 2012 UTC

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