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root/group/trunk/OOPSE-3.0/src/selection/SelectionEvaluator.cpp
Revision: 2102
Committed: Thu Mar 10 16:14:07 2005 UTC (19 years, 4 months ago) by tim
File size: 12785 byte(s)
Log Message:
minor change

File Contents

# Content
1 /*
2 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3 *
4 * The University of Notre Dame grants you ("Licensee") a
5 * non-exclusive, royalty free, license to use, modify and
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
19 * notice, this list of conditions and the following disclaimer.
20 *
21 * 3. Redistributions in binary form must reproduce the above copyright
22 * notice, this list of conditions and the following disclaimer in the
23 * documentation and/or other materials provided with the
24 * distribution.
25 *
26 * This software is provided "AS IS," without a warranty of any
27 * kind. All express or implied conditions, representations and
28 * warranties, including any implied warranty of merchantability,
29 * fitness for a particular purpose or non-infringement, are hereby
30 * excluded. The University of Notre Dame and its licensors shall not
31 * be liable for any damages suffered by licensee as a result of
32 * using, modifying or distributing the software or its
33 * derivatives. In no event will the University of Notre Dame or its
34 * licensors be liable for any lost revenue, profit or data, or for
35 * direct, indirect, special, consequential, incidental or punitive
36 * damages, however caused and regardless of the theory of liability,
37 * arising out of the use of or inability to use software, even if the
38 * University of Notre Dame has been advised of the possibility of
39 * such damages.
40 */
41
42 #include <stack>
43 #include "selection/SelectionEvaluator.hpp"
44 #include "primitives/Atom.hpp"
45 #include "primitives/DirectionalAtom.hpp"
46 #include "primitives/RigidBody.hpp"
47 #include "primitives/Molecule.hpp"
48
49 namespace oopse {
50
51
52 SelectionEvaluator::SelectionEvaluator(SimInfo* si)
53 : info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){
54
55 nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
56 }
57
58 bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
59 clearDefinitionsAndLoadPredefined();
60 this->filename = filename;
61 this->script = script;
62 if (! compiler.compile(filename, script)) {
63 error = true;
64 errorMessage = compiler.getErrorMessage();
65 std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
66 return false;
67 }
68
69 pc = 0;
70 aatoken = compiler.getAatokenCompiled();
71 linenumbers = compiler.getLineNumbers();
72 lineIndices = compiler.getLineIndices();
73
74 std::vector<std::vector<Token> >::const_iterator i;
75
76 isDynamic_ = false;
77 for (i = aatoken.begin(); i != aatoken.end(); ++i) {
78 if (containDynamicToken(*i)) {
79 isDynamic_ = true;
80 break;
81 }
82 }
83
84 isLoaded_ = true;
85 return true;
86 }
87
88 void SelectionEvaluator::clearState() {
89 error = false;
90 errorMessage = "";
91 }
92
93 bool SelectionEvaluator::loadScriptString(const std::string& script) {
94 clearState();
95 return loadScript("", script);
96 }
97
98 bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
99 clearState();
100 return loadScriptFileInternal(filename);
101 }
102
103 bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
104 std::ifstream ifs(filename.c_str());
105 if (!ifs.is_open()) {
106 return false;
107 }
108
109 const int bufferSize = 65535;
110 char buffer[bufferSize];
111 std::string script;
112 while(ifs.getline(buffer, bufferSize)) {
113 script += buffer;
114 }
115 return loadScript(filename, script);
116 }
117
118 void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
119
120 while ( pc < aatoken.size()) {
121 statement = aatoken[pc++];
122 statementLength = statement.size();
123 Token token = statement[0];
124 switch (token.tok) {
125 case Token::define:
126 define();
127 break;
128 case Token::select:
129 select(bs);
130 break;
131 default:
132 unrecognizedCommand(token);
133 return;
134 }
135 }
136
137 }
138
139 BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
140 BitSet bs;
141 std::stack<BitSet> stack;
142
143 for (int pc = pcStart; pc < code.size(); ++pc) {
144 Token instruction = code[pc];
145
146 switch (instruction.tok) {
147 case Token::expressionBegin:
148 break;
149 case Token::expressionEnd:
150 break;
151 case Token::all:
152 bs = BitSet(nStuntDouble);
153 bs.setAll();
154 stack.push(bs);
155 break;
156 case Token::none:
157 bs = BitSet(nStuntDouble);
158 stack.push(bs);
159 break;
160 case Token::opOr:
161 bs = stack.top();
162 stack.pop();
163 stack.top() |= bs;
164 break;
165 case Token::opAnd:
166 bs = stack.top();
167 stack.pop();
168 stack.top() &= bs;
169 break;
170 case Token::opNot:
171 stack.top().flip();
172 break;
173 case Token::within:
174
175 withinInstruction(instruction, stack.top());
176 break;
177 //case Token::selected:
178 // stack.push(getSelectionSet());
179 // break;
180 case Token::name:
181 stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
182 break;
183 case Token::index:
184 stack.push(indexInstruction(instruction.value));
185 break;
186 case Token::identifier:
187 stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
188 break;
189 case Token::opLT:
190 case Token::opLE:
191 case Token::opGE:
192 case Token::opGT:
193 case Token::opEQ:
194 case Token::opNE:
195 stack.push(comparatorInstruction(instruction));
196 break;
197 default:
198 unrecognizedExpression();
199 }
200 }
201 if (stack.size() != 1)
202 evalError("atom expression compiler error - stack over/underflow");
203
204 return stack.top();
205 }
206
207
208
209 BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
210 int comparator = instruction.tok;
211 int property = instruction.intValue;
212 float comparisonValue = boost::any_cast<float>(instruction.value);
213 float propertyValue;
214 BitSet bs(nStuntDouble);
215 bs.clearAll();
216
217 SimInfo::MoleculeIterator mi;
218 Molecule* mol;
219 Molecule::AtomIterator ai;
220 Atom* atom;
221 Molecule::RigidBodyIterator rbIter;
222 RigidBody* rb;
223
224 for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
225
226 for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
227 compareProperty(atom, bs, property, comparator, comparisonValue);
228 }
229
230 for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
231 compareProperty(rb, bs, property, comparator, comparisonValue);
232 }
233 }
234
235 return bs;
236 }
237
238 void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
239 double propertyValue;
240 switch (property) {
241 case Token::mass:
242 propertyValue = sd->getMass();
243 break;
244 case Token::charge:
245 return;
246 //break;
247 case Token::dipole:
248 return;
249 //break;
250 default:
251 unrecognizedAtomProperty(property);
252 }
253
254 bool match = false;
255 switch (comparator) {
256 case Token::opLT:
257 match = propertyValue < comparisonValue;
258 break;
259 case Token::opLE:
260 match = propertyValue <= comparisonValue;
261 break;
262 case Token::opGE:
263 match = propertyValue >= comparisonValue;
264 break;
265 case Token::opGT:
266 match = propertyValue > comparisonValue;
267 break;
268 case Token::opEQ:
269 match = propertyValue == comparisonValue;
270 break;
271 case Token::opNE:
272 match = propertyValue != comparisonValue;
273 break;
274 }
275 if (match)
276 bs.setBitOn(sd->getGlobalIndex());
277
278 }
279
280 void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs){
281
282 boost::any withinSpec = instruction.value;
283 float distance;
284 if (withinSpec.type() == typeid(float)){
285 distance = boost::any_cast<float>(withinSpec);
286 } else if (withinSpec.type() == typeid(int)) {
287 distance = boost::any_cast<int>(withinSpec);
288 } else {
289 evalError("casting error in withinInstruction");
290 bs.clearAll();
291 }
292
293 bs = distanceFinder.find(bs, distance);
294 }
295
296 void SelectionEvaluator::define() {
297 assert(statement.size() >= 3);
298
299 std::string variable = boost::any_cast<std::string>(statement[1].value);
300
301 variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
302 }
303
304
305 /** @todo */
306 void SelectionEvaluator::predefine(const std::string& script) {
307
308 if (compiler.compile("#predefine", script)) {
309 std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
310 if (aatoken.size() != 1) {
311 evalError("predefinition does not have exactly 1 command:"
312 + script);
313 return;
314 }
315 std::vector<Token> statement = aatoken[0];
316 if (statement.size() > 2) {
317 int tok = statement[1].tok;
318 if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
319 std::string variable = boost::any_cast<std::string>(statement[1].value);
320 variables.insert(VariablesType::value_type(variable, statement));
321
322 } else {
323 evalError("invalid variable name:" + script);
324 }
325 }else {
326 evalError("bad predefinition length:" + script);
327 }
328
329
330 } else {
331 evalError("predefined set compile error:" + script +
332 "\ncompile error:" + compiler.getErrorMessage());
333 }
334
335 }
336
337 void SelectionEvaluator::select(BitSet& bs){
338 bs = expression(statement, 1);
339 }
340
341 BitSet SelectionEvaluator::lookupValue(const std::string& variable){
342
343 BitSet bs(nStuntDouble);
344 std::map<std::string, boost::any>::iterator i = variables.find(variable);
345
346 if (i != variables.end()) {
347 if (i->second.type() == typeid(BitSet)) {
348 return boost::any_cast<BitSet>(i->second);
349 } else if (i->second.type() == typeid(std::vector<Token>)){
350 bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
351 i->second = bs; /**@todo fixme */
352 return bs;
353 }
354 } else {
355 unrecognizedIdentifier(variable);
356 }
357
358 return bs;
359 }
360
361 BitSet SelectionEvaluator::nameInstruction(const std::string& name){
362
363 return nameFinder.match(name);
364
365 }
366
367 bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
368 std::vector<Token>::const_iterator i;
369 for (i = tokens.begin(); i != tokens.end(); ++i) {
370 if (i->tok & Token::dynamic) {
371 return true;
372 }
373 }
374
375 return false;
376 }
377
378 void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
379 variables.clear();
380 //load predefine
381 //predefine();
382 }
383
384 BitSet SelectionEvaluator::evaluate() {
385 BitSet bs(nStuntDouble);
386 if (isLoaded_) {
387 pc = 0;
388 instructionDispatchLoop(bs);
389 }
390
391 return bs;
392 }
393
394 BitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
395 BitSet bs(nStuntDouble);
396
397 if (value.type() == typeid(int)) {
398 int index = boost::any_cast<int>(value);
399 if (index < 0 || index >= bs.size()) {
400 invalidIndex(index);
401 } else {
402 bs = indexFinder.find(index);
403 }
404 } else if (value.type() == typeid(std::pair<int, int>)) {
405 std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
406 assert(indexRange.first <= indexRange.second);
407 if (indexRange.first < 0 || indexRange.second >= bs.size()) {
408 invalidIndexRange(indexRange);
409 }else {
410 bs = indexFinder.find(indexRange.first, indexRange.second);
411 }
412 }
413
414 return bs;
415 }
416
417 }