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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 1412 by gezelter, Mon Mar 22 18:45:39 2010 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>
# 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 {
50 > namespace OpenMD {
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), hullFinder(info),
55 >      indexFinder(info),
56 >      isLoaded_(false){    
57 >      nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
58      }            
59  
60 <  bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
60 >  bool SelectionEvaluator::loadScript(const std::string& filename,
61 >                                      const std::string& script) {
62      clearDefinitionsAndLoadPredefined();
63      this->filename = filename;
64      this->script = script;
65      if (! compiler.compile(filename, script)) {
66        error = true;
67        errorMessage = compiler.getErrorMessage();
68 <      std::cerr << "SelectionCompiler Error: " << errorMessage << std::endl;
68 >
69 >      sprintf( painCave.errMsg,
70 >               "SelectionCompiler Error: %s\n", errorMessage.c_str());
71 >      painCave.severity = OPENMD_ERROR;
72 >      painCave.isFatal = 1;
73 >      simError();
74        return false;
75      }
76  
# Line 100 | Line 108 | namespace oopse {
108      return loadScriptFileInternal(filename);
109    }
110  
111 <  bool SelectionEvaluator::loadScriptFileInternal(const  std::string & filename) {
112 <    std::ifstream ifs(filename.c_str());
111 >  bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
112 >    ifstrstream ifs(filename.c_str());
113      if (!ifs.is_open()) {
114        return false;
115      }
116 <
116 >    
117      const int bufferSize = 65535;
118      char buffer[bufferSize];
119      std::string script;
# Line 114 | Line 122 | namespace oopse {
122      }
123      return loadScript(filename, script);
124    }
125 <
126 <  void SelectionEvaluator::instructionDispatchLoop(OOPSEBitSet& bs){
125 >  
126 >  void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
127      
128      while ( pc < aatoken.size()) {
129        statement = aatoken[pc++];
# Line 136 | Line 144 | namespace oopse {
144  
145    }
146  
147 <  OOPSEBitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
148 <    OOPSEBitSet bs;
149 <    std::stack<OOPSEBitSet> stack;
150 <    
147 >  OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
148 >                                             int pcStart) {
149 >    OpenMDBitSet bs;
150 >    std::stack<OpenMDBitSet> stack;
151 >  
152      for (int pc = pcStart; pc < code.size(); ++pc) {
153        Token instruction = code[pc];
154  
# Line 149 | Line 158 | namespace oopse {
158        case Token::expressionEnd:
159          break;
160        case Token::all:
161 <        bs = OOPSEBitSet(nStuntDouble);
161 >        bs = OpenMDBitSet(nStuntDouble);
162          bs.setAll();
163          stack.push(bs);            
164          break;
165        case Token::none:
166 <        bs = OOPSEBitSet(nStuntDouble);
166 >        bs = OpenMDBitSet(nStuntDouble);
167          stack.push(bs);            
168          break;
169        case Token::opOr:
# Line 171 | Line 180 | namespace oopse {
180          stack.top().flip();
181          break;
182        case Token::within:
174 –
183          withinInstruction(instruction, stack.top());
184          break;
185 +      case Token::hull:
186 +        stack.push(hull());
187 +        break;
188          //case Token::selected:
189          //  stack.push(getSelectionSet());
190          //  break;
# Line 206 | Line 217 | namespace oopse {
217  
218  
219  
220 <  OOPSEBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
220 >  OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
221      int comparator = instruction.tok;
222      int property = instruction.intValue;
223      float comparisonValue = boost::any_cast<float>(instruction.value);
224      float propertyValue;
225 <    OOPSEBitSet bs(nStuntDouble);
225 >    OpenMDBitSet bs(nStuntDouble);
226      bs.clearAll();
227      
228      SimInfo::MoleculeIterator mi;
# Line 220 | Line 231 | namespace oopse {
231      Atom* atom;
232      Molecule::RigidBodyIterator rbIter;
233      RigidBody* rb;
223 –    
224 –    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
234  
235 +    for (mol = info->beginMolecule(mi); mol != NULL;
236 +         mol = info->nextMolecule(mi)) {
237 +
238        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
239          compareProperty(atom, bs, property, comparator, comparisonValue);
240        }
241 <        
242 <      for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
243 <        compareProperty(rb, bs, property, comparator, comparisonValue);
244 <      }        
241 >    
242 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
243 >           rb = mol->nextRigidBody(rbIter)) {
244 >        compareProperty(rb, bs, property, comparator, comparisonValue);
245 >      }
246      }
247  
248      return bs;
249    }
250  
251 <  void SelectionEvaluator::compareProperty(StuntDouble* sd, OOPSEBitSet& bs, int property, int comparator, float comparisonValue) {
252 <    double propertyValue = 0.0;
251 >  void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
252 >                                           int property, int comparator,
253 >                                           float comparisonValue) {
254 >    RealType propertyValue = 0.0;
255      switch (property) {
256      case Token::mass:
257        propertyValue = sd->getMass();
# Line 254 | Line 269 | namespace oopse {
269          }
270        }
271        break;
272 +    case Token::x:
273 +      propertyValue = sd->getPos().x();
274 +      break;
275 +    case Token::y:
276 +      propertyValue = sd->getPos().y();
277 +      break;
278 +    case Token::z:
279 +      propertyValue = sd->getPos().z();
280 +      break;
281      default:
282        unrecognizedAtomProperty(property);
283      }
# Line 281 | Line 305 | namespace oopse {
305      }
306      if (match)
307        bs.setBitOn(sd->getGlobalIndex());
308 <
308 >    
309    }
310  
311 <  void SelectionEvaluator::withinInstruction(const Token& instruction, OOPSEBitSet& bs){
311 >  void SelectionEvaluator::withinInstruction(const Token& instruction,
312 >                                             OpenMDBitSet& bs){
313      
314      boost::any withinSpec = instruction.value;
315      float distance;
# Line 299 | Line 324 | namespace oopse {
324      
325      bs = distanceFinder.find(bs, distance);            
326    }
327 <
327 >  
328    void SelectionEvaluator::define() {
329      assert(statement.size() >= 3);
330 <
330 >    
331      std::string variable = boost::any_cast<std::string>(statement[1].value);
332 <
333 <    variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
332 >    
333 >    variables.insert(VariablesType::value_type(variable,
334 >                                               expression(statement, 2)));
335    }
336 +  
337  
311 –
338    /** @todo */
339    void SelectionEvaluator::predefine(const std::string& script) {
340 <
340 >    
341      if (compiler.compile("#predefine", script)) {
342        std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
343        if (aatoken.size() != 1) {
# Line 322 | Line 348 | namespace oopse {
348        std::vector<Token> statement = aatoken[0];
349        if (statement.size() > 2) {
350          int tok = statement[1].tok;
351 <        if (tok == Token::identifier || (tok & Token::predefinedset) == Token::predefinedset) {
351 >        if (tok == Token::identifier ||
352 >            (tok & Token::predefinedset) == Token::predefinedset) {
353            std::string variable = boost::any_cast<std::string>(statement[1].value);
354            variables.insert(VariablesType::value_type(variable, statement));
355 <
355 >          
356          } else {
357            evalError("invalid variable name:" + script);
358          }
359        }else {
360          evalError("bad predefinition length:" + script);
361 <      }
335 <
361 >      }      
362          
363      } else {
364        evalError("predefined set compile error:" + script +
365                  "\ncompile error:" + compiler.getErrorMessage());
366      }
341 –
367    }
368  
369 <  void SelectionEvaluator::select(OOPSEBitSet& bs){
369 >  void SelectionEvaluator::select(OpenMDBitSet& bs){
370      bs = expression(statement, 1);
371    }
372 <
373 <  OOPSEBitSet SelectionEvaluator::lookupValue(const std::string& variable){
374 <
375 <    OOPSEBitSet bs(nStuntDouble);
372 >  
373 >  OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
374 >    
375 >    OpenMDBitSet bs(nStuntDouble);
376      std::map<std::string, boost::any>::iterator i = variables.find(variable);
377      
378      if (i != variables.end()) {
379 <      if (i->second.type() == typeid(OOPSEBitSet)) {
380 <        return boost::any_cast<OOPSEBitSet>(i->second);
379 >      if (i->second.type() == typeid(OpenMDBitSet)) {
380 >        return boost::any_cast<OpenMDBitSet>(i->second);
381        } else if (i->second.type() ==  typeid(std::vector<Token>)){
382          bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2);
383          i->second =  bs; /**@todo fixme */
# Line 361 | Line 386 | namespace oopse {
386      } else {
387        unrecognizedIdentifier(variable);
388      }
389 <
389 >    
390      return bs;
391    }
392 <
393 <  OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){
394 <    
370 <    return nameFinder.match(name);
371 <
392 >  
393 >  OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){    
394 >    return nameFinder.match(name);    
395    }    
396  
397    bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
# Line 378 | Line 401 | namespace oopse {
401          return true;
402        }
403      }
404 <
404 >    
405      return false;
406    }    
407  
# Line 388 | Line 411 | namespace oopse {
411      //predefine();
412    }
413  
414 <  OOPSEBitSet SelectionEvaluator::evaluate() {
415 <    OOPSEBitSet bs(nStuntDouble);
414 >  OpenMDBitSet SelectionEvaluator::evaluate() {
415 >    OpenMDBitSet bs(nStuntDouble);
416      if (isLoaded_) {
417        pc = 0;
418        instructionDispatchLoop(bs);
# Line 398 | Line 421 | namespace oopse {
421      return bs;
422    }
423  
424 <  OOPSEBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
425 <    OOPSEBitSet bs(nStuntDouble);
424 >  OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
425 >    OpenMDBitSet bs(nStuntDouble);
426  
427      if (value.type() == typeid(int)) {
428        int index = boost::any_cast<int>(value);
# Line 422 | Line 445 | namespace oopse {
445    }
446  
447  
448 <  double SelectionEvaluator::getCharge(Atom* atom) {
449 <    double charge =0.0;
448 >  OpenMDBitSet SelectionEvaluator::hull() {
449 >    OpenMDBitSet bs(nStuntDouble);
450 >    
451 >    bs = hullFinder.findHull();
452 >    
453 >    return bs;
454 >  }
455 >
456 >
457 >
458 >  RealType SelectionEvaluator::getCharge(Atom* atom) {
459 >    RealType charge =0.0;
460      AtomType* atomType = atom->getAtomType();
461      if (atomType->isCharge()) {
462        GenericData* data = atomType->getPropertyByName("Charge");
# Line 436 | Line 469 | namespace oopse {
469          } else {
470            sprintf( painCave.errMsg,
471                     "Can not cast GenericData to DoubleGenericData\n");
472 <          painCave.severity = OOPSE_ERROR;
472 >          painCave.severity = OPENMD_ERROR;
473            painCave.isFatal = 1;
474            simError();          
475          }

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