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root/OpenMD/trunk/src/selection/SelectionEvaluator.cpp
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Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
Revision 1364 by cli2, Wed Oct 7 20:49:50 2009 UTC

# Line 45 | Line 45
45   #include "primitives/DirectionalAtom.hpp"
46   #include "primitives/RigidBody.hpp"
47   #include "primitives/Molecule.hpp"
48 + #include "io/basic_ifstrstream.hpp"
49  
50   namespace oopse {
51  
52  
53    SelectionEvaluator::SelectionEvaluator(SimInfo* si)
54 <    : info(si), nameFinder(info), distanceFinder(info), indexFinder(info), isLoaded_(false){
55 <    
56 <      nStuntDouble = info->getNGlobalAtoms() + info->getNRigidBodies();
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, const std::string& script) {
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 <      std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
67 >
68 >      sprintf( painCave.errMsg,
69 >               "SelectionCompiler Error: %s\n", errorMessage.c_str());
70 >      painCave.severity = OOPSE_ERROR;
71 >      painCave.isFatal = 1;
72 >      simError();
73        return false;
74      }
75  
# Line 100 | Line 107 | namespace oopse {
107      return loadScriptFileInternal(filename);
108    }
109  
110 <  bool SelectionEvaluator::loadScriptFileInternal(const  std::string & filename) {
111 <    std::ifstream ifs(filename.c_str());
110 >  bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
111 >    ifstrstream ifs(filename.c_str());
112      if (!ifs.is_open()) {
113        return false;
114      }
115 <
115 >    
116      const int bufferSize = 65535;
117      char buffer[bufferSize];
118      std::string script;
# Line 114 | Line 121 | namespace oopse {
121      }
122      return loadScript(filename, script);
123    }
124 <
124 >  
125    void SelectionEvaluator::instructionDispatchLoop(OOPSEBitSet& bs){
126      
127      while ( pc < aatoken.size()) {
# Line 136 | Line 143 | namespace oopse {
143  
144    }
145  
146 <  OOPSEBitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
146 >  OOPSEBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
147 >                                             int pcStart) {
148      OOPSEBitSet bs;
149 <    std::stack<OOPSEBitSet> stack;
150 <    
149 >    std::stack<OOPSEBitSet> stack;
150 >  
151      for (int pc = pcStart; pc < code.size(); ++pc) {
152        Token instruction = code[pc];
153  
# Line 171 | Line 179 | namespace oopse {
179          stack.top().flip();
180          break;
181        case Token::within:
174 –
182          withinInstruction(instruction, stack.top());
183          break;
184          //case Token::selected:
# Line 220 | Line 227 | namespace oopse {
227      Atom* atom;
228      Molecule::RigidBodyIterator rbIter;
229      RigidBody* rb;
223 –    
224 –    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
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; rb = mol->nextRigidBody(rbIter)) {
239 <        compareProperty(rb, bs, property, comparator, comparisonValue);
240 <      }        
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, OOPSEBitSet& bs, int property, int comparator, float comparisonValue) {
248 <    double propertyValue = 0.0;
247 >  void SelectionEvaluator::compareProperty(StuntDouble* sd, OOPSEBitSet& 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();
# Line 254 | Line 265 | namespace oopse {
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      }
# Line 281 | Line 301 | namespace oopse {
301      }
302      if (match)
303        bs.setBitOn(sd->getGlobalIndex());
304 <
304 >    
305    }
306  
307 <  void SelectionEvaluator::withinInstruction(const Token& instruction, OOPSEBitSet& bs){
307 >  void SelectionEvaluator::withinInstruction(const Token& instruction,
308 >                                             OOPSEBitSet& bs){
309      
310      boost::any withinSpec = instruction.value;
311      float distance;
# Line 299 | Line 320 | namespace oopse {
320      
321      bs = distanceFinder.find(bs, distance);            
322    }
323 <
323 >  
324    void SelectionEvaluator::define() {
325      assert(statement.size() >= 3);
326 <
326 >    
327      std::string variable = boost::any_cast<std::string>(statement[1].value);
328 <
329 <    variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
328 >    
329 >    variables.insert(VariablesType::value_type(variable,
330 >                                               expression(statement, 2)));
331    }
332 +  
333  
311 –
334    /** @todo */
335    void SelectionEvaluator::predefine(const std::string& script) {
336 <
336 >    
337      if (compiler.compile("#predefine", script)) {
338        std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
339        if (aatoken.size() != 1) {
# Line 322 | Line 344 | namespace oopse {
344        std::vector<Token> statement = aatoken[0];
345        if (statement.size() > 2) {
346          int tok = statement[1].tok;
347 <        if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
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 <
351 >          
352          } else {
353            evalError("invalid variable name:" + script);
354          }
355        }else {
356          evalError("bad predefinition length:" + script);
357 <      }
335 <
357 >      }      
358          
359      } else {
360        evalError("predefined set compile error:" + script +
361                  "\ncompile error:" + compiler.getErrorMessage());
362      }
341 –
363    }
364  
365    void SelectionEvaluator::select(OOPSEBitSet& bs){
366      bs = expression(statement, 1);
367    }
368 <
368 >  
369    OOPSEBitSet SelectionEvaluator::lookupValue(const std::string& variable){
370 <
370 >    
371      OOPSEBitSet bs(nStuntDouble);
372      std::map<std::string, boost::any>::iterator i = variables.find(variable);
373      
# Line 361 | Line 382 | namespace oopse {
382      } else {
383        unrecognizedIdentifier(variable);
384      }
385 <
385 >    
386      return bs;
387    }
388 <
389 <  OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){
390 <    
370 <    return nameFinder.match(name);
371 <
388 >  
389 >  OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){    
390 >    return nameFinder.match(name);    
391    }    
392  
393    bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
# Line 378 | Line 397 | namespace oopse {
397          return true;
398        }
399      }
400 <
400 >    
401      return false;
402    }    
403  
# Line 422 | Line 441 | namespace oopse {
441    }
442  
443  
444 <  double SelectionEvaluator::getCharge(Atom* atom) {
445 <    double charge =0.0;
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");

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