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Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 277 by tim, Tue Feb 1 06:55:00 2005 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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]  Vardeman & Gezelter, in progress (2009).                        
40   */
41  
42 + #include <stack>
43   #include "selection/SelectionEvaluator.hpp"
44 < namespace oopse {
44 > #include "primitives/Atom.hpp"
45 > #include "primitives/DirectionalAtom.hpp"
46 > #include "primitives/RigidBody.hpp"
47 > #include "primitives/Molecule.hpp"
48 > #include "io/basic_ifstrstream.hpp"
49 >
50 > namespace OpenMD {
51 >
52 >
53 >  SelectionEvaluator::SelectionEvaluator(SimInfo* si)
54 >    : info(si), nameFinder(info), distanceFinder(info), indexFinder(info),
55 >      isLoaded_(false){    
56 >      nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
57 >    }            
58 >
59 >  bool SelectionEvaluator::loadScript(const std::string& filename,
60 >                                      const std::string& script) {
61 >    clearDefinitionsAndLoadPredefined();
62 >    this->filename = filename;
63 >    this->script = script;
64 >    if (! compiler.compile(filename, script)) {
65 >      error = true;
66 >      errorMessage = compiler.getErrorMessage();
67 >
68 >      sprintf( painCave.errMsg,
69 >               "SelectionCompiler Error: %s\n", errorMessage.c_str());
70 >      painCave.severity = OPENMD_ERROR;
71 >      painCave.isFatal = 1;
72 >      simError();
73 >      return false;
74 >    }
75 >
76 >    pc = 0;
77 >    aatoken = compiler.getAatokenCompiled();
78 >    linenumbers = compiler.getLineNumbers();
79 >    lineIndices = compiler.getLineIndices();
80 >
81 >    std::vector<std::vector<Token> >::const_iterator i;  
82 >
83 >    isDynamic_ = false;
84 >    for (i = aatoken.begin(); i != aatoken.end(); ++i) {
85 >      if (containDynamicToken(*i)) {
86 >        isDynamic_ = true;
87 >        break;
88 >      }
89 >    }
90 >
91 >    isLoaded_ = true;
92 >    return true;
93 >  }
94 >
95 >  void SelectionEvaluator::clearState() {
96 >    error = false;
97 >    errorMessage = "";
98 >  }
99 >
100 >  bool SelectionEvaluator::loadScriptString(const std::string& script) {
101 >    clearState();
102 >    return loadScript("", script);
103 >  }
104 >
105 >  bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
106 >    clearState();
107 >    return loadScriptFileInternal(filename);
108 >  }
109 >
110 >  bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
111 >    ifstrstream ifs(filename.c_str());
112 >    if (!ifs.is_open()) {
113 >      return false;
114 >    }
115 >    
116 >    const int bufferSize = 65535;
117 >    char buffer[bufferSize];
118 >    std::string script;
119 >    while(ifs.getline(buffer, bufferSize)) {
120 >      script += buffer;
121 >    }
122 >    return loadScript(filename, script);
123 >  }
124 >  
125 >  void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
126 >    
127 >    while ( pc < aatoken.size()) {
128 >      statement = aatoken[pc++];
129 >      statementLength = statement.size();
130 >      Token token = statement[0];
131 >      switch (token.tok) {
132 >      case Token::define:
133 >        define();
134 >        break;
135 >      case Token::select:
136 >        select(bs);
137 >        break;
138 >      default:
139 >        unrecognizedCommand(token);
140 >        return;
141 >      }
142 >    }
143 >
144 >  }
145 >
146 >  OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
147 >                                             int pcStart) {
148 >    OpenMDBitSet bs;
149 >    std::stack<OpenMDBitSet> stack;
150 >  
151 >    for (int pc = pcStart; pc < code.size(); ++pc) {
152 >      Token instruction = code[pc];
153 >
154 >      switch (instruction.tok) {
155 >      case Token::expressionBegin:
156 >        break;
157 >      case Token::expressionEnd:
158 >        break;
159 >      case Token::all:
160 >        bs = OpenMDBitSet(nStuntDouble);
161 >        bs.setAll();
162 >        stack.push(bs);            
163 >        break;
164 >      case Token::none:
165 >        bs = OpenMDBitSet(nStuntDouble);
166 >        stack.push(bs);            
167 >        break;
168 >      case Token::opOr:
169 >        bs = stack.top();
170 >        stack.pop();
171 >        stack.top() |= bs;
172 >        break;
173 >      case Token::opAnd:
174 >        bs = stack.top();
175 >        stack.pop();
176 >        stack.top() &= bs;
177 >        break;
178 >      case Token::opNot:
179 >        stack.top().flip();
180 >        break;
181 >      case Token::within:
182 >        withinInstruction(instruction, stack.top());
183 >        break;
184 >        //case Token::selected:
185 >        //  stack.push(getSelectionSet());
186 >        //  break;
187 >      case Token::name:
188 >        stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
189 >        break;
190 >      case Token::index:
191 >        stack.push(indexInstruction(instruction.value));
192 >        break;
193 >      case Token::identifier:
194 >        stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
195 >        break;
196 >      case Token::opLT:
197 >      case Token::opLE:
198 >      case Token::opGE:
199 >      case Token::opGT:
200 >      case Token::opEQ:
201 >      case Token::opNE:
202 >        stack.push(comparatorInstruction(instruction));
203 >        break;
204 >      default:
205 >        unrecognizedExpression();
206 >      }
207 >    }
208 >    if (stack.size() != 1)
209 >      evalError("atom expression compiler error - stack over/underflow");
210 >          
211 >    return stack.top();
212 >  }
213 >
214 >
215 >
216 >  OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
217 >    int comparator = instruction.tok;
218 >    int property = instruction.intValue;
219 >    float comparisonValue = boost::any_cast<float>(instruction.value);
220 >    float propertyValue;
221 >    OpenMDBitSet bs(nStuntDouble);
222 >    bs.clearAll();
223 >    
224 >    SimInfo::MoleculeIterator mi;
225 >    Molecule* mol;
226 >    Molecule::AtomIterator ai;
227 >    Atom* atom;
228 >    Molecule::RigidBodyIterator rbIter;
229 >    RigidBody* rb;
230 >
231 >    for (mol = info->beginMolecule(mi); mol != NULL;
232 >         mol = info->nextMolecule(mi)) {
233 >
234 >      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
235 >        compareProperty(atom, bs, property, comparator, comparisonValue);
236 >      }
237 >    
238 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
239 >           rb = mol->nextRigidBody(rbIter)) {
240 >        compareProperty(rb, bs, property, comparator, comparisonValue);
241 >      }
242 >    }
243 >
244 >    return bs;
245 >  }
246  
247 +  void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
248 +                                           int property, int comparator,
249 +                                           float comparisonValue) {
250 +    RealType propertyValue = 0.0;
251 +    switch (property) {
252 +    case Token::mass:
253 +      propertyValue = sd->getMass();
254 +      break;
255 +    case Token::charge:
256 +      if (sd->isAtom()){
257 +        Atom* atom = static_cast<Atom*>(sd);
258 +        propertyValue = getCharge(atom);
259 +      } else if (sd->isRigidBody()) {
260 +        RigidBody* rb = static_cast<RigidBody*>(sd);
261 +        RigidBody::AtomIterator ai;
262 +        Atom* atom;
263 +        for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
264 +          propertyValue+=  getCharge(atom);
265 +        }
266 +      }
267 +      break;
268 +    case Token::x:
269 +      propertyValue = sd->getPos().x();
270 +      break;
271 +    case Token::y:
272 +      propertyValue = sd->getPos().y();
273 +      break;
274 +    case Token::z:
275 +      propertyValue = sd->getPos().z();
276 +      break;
277 +    default:
278 +      unrecognizedAtomProperty(property);
279 +    }
280 +        
281 +    bool match = false;
282 +    switch (comparator) {
283 +    case Token::opLT:
284 +      match = propertyValue < comparisonValue;
285 +      break;
286 +    case Token::opLE:
287 +      match = propertyValue <= comparisonValue;
288 +      break;
289 +    case Token::opGE:
290 +      match = propertyValue >= comparisonValue;
291 +      break;
292 +    case Token::opGT:
293 +      match = propertyValue > comparisonValue;
294 +      break;
295 +    case Token::opEQ:
296 +      match = propertyValue == comparisonValue;
297 +      break;
298 +    case Token::opNE:
299 +      match = propertyValue != comparisonValue;
300 +      break;
301 +    }
302 +    if (match)
303 +      bs.setBitOn(sd->getGlobalIndex());
304 +    
305 +  }
306  
307 +  void SelectionEvaluator::withinInstruction(const Token& instruction,
308 +                                             OpenMDBitSet& bs){
309 +    
310 +    boost::any withinSpec = instruction.value;
311 +    float distance;
312 +    if (withinSpec.type() == typeid(float)){
313 +      distance = boost::any_cast<float>(withinSpec);
314 +    } else if (withinSpec.type() == typeid(int)) {
315 +      distance = boost::any_cast<int>(withinSpec);    
316 +    } else {
317 +      evalError("casting error in withinInstruction");
318 +      bs.clearAll();
319 +    }
320 +    
321 +    bs = distanceFinder.find(bs, distance);            
322 +  }
323 +  
324 +  void SelectionEvaluator::define() {
325 +    assert(statement.size() >= 3);
326 +    
327 +    std::string variable = boost::any_cast<std::string>(statement[1].value);
328 +    
329 +    variables.insert(VariablesType::value_type(variable,
330 +                                               expression(statement, 2)));
331 +  }
332 +  
333 +
334 +  /** @todo */
335 +  void SelectionEvaluator::predefine(const std::string& script) {
336 +    
337 +    if (compiler.compile("#predefine", script)) {
338 +      std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
339 +      if (aatoken.size() != 1) {
340 +        evalError("predefinition does not have exactly 1 command:"
341 +                  + script);
342 +        return;
343 +      }
344 +      std::vector<Token> statement = aatoken[0];
345 +      if (statement.size() > 2) {
346 +        int tok = statement[1].tok;
347 +        if (tok == Token::identifier ||
348 +            (tok & Token::predefinedset) == Token::predefinedset) {
349 +          std::string variable = boost::any_cast<std::string>(statement[1].value);
350 +          variables.insert(VariablesType::value_type(variable, statement));
351 +          
352 +        } else {
353 +          evalError("invalid variable name:" + script);
354 +        }
355 +      }else {
356 +        evalError("bad predefinition length:" + script);
357 +      }      
358 +        
359 +    } else {
360 +      evalError("predefined set compile error:" + script +
361 +                "\ncompile error:" + compiler.getErrorMessage());
362 +    }
363 +  }
364 +
365 +  void SelectionEvaluator::select(OpenMDBitSet& bs){
366 +    bs = expression(statement, 1);
367 +  }
368 +  
369 +  OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
370 +    
371 +    OpenMDBitSet bs(nStuntDouble);
372 +    std::map<std::string, boost::any>::iterator i = variables.find(variable);
373 +    
374 +    if (i != variables.end()) {
375 +      if (i->second.type() == typeid(OpenMDBitSet)) {
376 +        return boost::any_cast<OpenMDBitSet>(i->second);
377 +      } else if (i->second.type() ==  typeid(std::vector<Token>)){
378 +        bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
379 +        i->second =  bs; /**@todo fixme */
380 +        return bs;
381 +      }
382 +    } else {
383 +      unrecognizedIdentifier(variable);
384 +    }
385 +    
386 +    return bs;
387 +  }
388 +  
389 +  OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){    
390 +    return nameFinder.match(name);    
391 +  }    
392 +
393 +  bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
394 +    std::vector<Token>::const_iterator i;
395 +    for (i = tokens.begin(); i != tokens.end(); ++i) {
396 +      if (i->tok & Token::dynamic) {
397 +        return true;
398 +      }
399 +    }
400 +    
401 +    return false;
402 +  }    
403 +
404 +  void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
405 +    variables.clear();
406 +    //load predefine
407 +    //predefine();
408 +  }
409 +
410 +  OpenMDBitSet SelectionEvaluator::evaluate() {
411 +    OpenMDBitSet bs(nStuntDouble);
412 +    if (isLoaded_) {
413 +      pc = 0;
414 +      instructionDispatchLoop(bs);
415 +    }
416 +
417 +    return bs;
418 +  }
419 +
420 +  OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
421 +    OpenMDBitSet bs(nStuntDouble);
422 +
423 +    if (value.type() == typeid(int)) {
424 +      int index = boost::any_cast<int>(value);
425 +      if (index < 0 || index >= bs.size()) {
426 +        invalidIndex(index);
427 +      } else {
428 +        bs = indexFinder.find(index);
429 +      }
430 +    } else if (value.type() == typeid(std::pair<int, int>)) {
431 +      std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
432 +      assert(indexRange.first <= indexRange.second);
433 +      if (indexRange.first < 0 || indexRange.second >= bs.size()) {
434 +        invalidIndexRange(indexRange);
435 +      }else {
436 +        bs = indexFinder.find(indexRange.first, indexRange.second);
437 +      }
438 +    }
439 +
440 +    return bs;
441 +  }
442 +
443 +
444 +  RealType SelectionEvaluator::getCharge(Atom* atom) {
445 +    RealType charge =0.0;
446 +    AtomType* atomType = atom->getAtomType();
447 +    if (atomType->isCharge()) {
448 +      GenericData* data = atomType->getPropertyByName("Charge");
449 +      if (data != NULL) {
450 +        DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
451 +
452 +        if (doubleData != NULL) {
453 +          charge = doubleData->getData();
454 +
455 +        } else {
456 +          sprintf( painCave.errMsg,
457 +                   "Can not cast GenericData to DoubleGenericData\n");
458 +          painCave.severity = OPENMD_ERROR;
459 +          painCave.isFatal = 1;
460 +          simError();          
461 +        }
462 +      }
463 +    }
464 +
465 +    return charge;
466 +  }
467 +
468   }

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