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root/OpenMD/trunk/src/selection/SelectionEvaluator.cpp
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Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 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>
# 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();
57 < }            
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, 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;
68 <        return false;
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;
# Line 75 | Line 82 | bool SelectionEvaluator::loadScript(const std::string&
82  
83      isDynamic_ = false;
84      for (i = aatoken.begin(); i != aatoken.end(); ++i) {
85 <        if (containDynamicToken(*i)) {
86 <            isDynamic_ = true;
87 <            break;
88 <        }
85 >      if (containDynamicToken(*i)) {
86 >        isDynamic_ = true;
87 >        break;
88 >      }
89      }
90  
91      isLoaded_ = true;
92      return true;
93 < }
93 >  }
94  
95 < void SelectionEvaluator::clearState() {
89 <    //for (int i = scriptLevelMax; --i >= 0; )
90 <    //    stack[i].clear();
91 <    //scriptLevel = 0;
95 >  void SelectionEvaluator::clearState() {
96      error = false;
97      errorMessage = "";
98 < }
98 >  }
99  
100 < bool SelectionEvaluator::loadScriptString(const std::string& script) {
100 >  bool SelectionEvaluator::loadScriptString(const std::string& script) {
101      clearState();
102      return loadScript("", script);
103 < }
103 >  }
104  
105 < bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
105 >  bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
106      clearState();
107      return loadScriptFileInternal(filename);
108 < }
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;
113 >      return false;
114      }
115 <
115 >    
116      const int bufferSize = 65535;
117      char buffer[bufferSize];
118      std::string script;
119      while(ifs.getline(buffer, bufferSize)) {
120 <        script += buffer;
120 >      script += buffer;
121      }
122      return loadScript(filename, script);
123 < }
124 <
125 < void SelectionEvaluator::instructionDispatchLoop(BitSet& bs){
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 <        }
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 < }
144 >  }
145  
146 <  BitSet SelectionEvaluator::expression(const std::vector<Token>& code, int pcStart) {
147 <    BitSet bs;
148 <    std::stack<BitSet> stack;
149 <    
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  
# Line 152 | Line 157 | void SelectionEvaluator::instructionDispatchLoop(BitSe
157        case Token::expressionEnd:
158          break;
159        case Token::all:
160 <        bs = BitSet(nStuntDouble);
160 >        bs = OpenMDBitSet(nStuntDouble);
161          bs.setAll();
162          stack.push(bs);            
163          break;
164        case Token::none:
165 <        bs = BitSet(nStuntDouble);
165 >        bs = OpenMDBitSet(nStuntDouble);
166          stack.push(bs);            
167          break;
168        case Token::opOr:
# Line 174 | Line 179 | void SelectionEvaluator::instructionDispatchLoop(BitSe
179          stack.top().flip();
180          break;
181        case Token::within:
177 –
182          withinInstruction(instruction, stack.top());
183          break;
184 <      //case Token::selected:
185 <      //  stack.push(getSelectionSet());
186 <      //  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;
# Line 209 | Line 213 | void SelectionEvaluator::instructionDispatchLoop(BitSe
213  
214  
215  
216 < BitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
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 <    BitSet bs(nStuntDouble);
221 >    OpenMDBitSet bs(nStuntDouble);
222      bs.clearAll();
223      
224      SimInfo::MoleculeIterator mi;
# Line 223 | Line 227 | BitSet SelectionEvaluator::comparatorInstruction(const
227      Atom* atom;
228      Molecule::RigidBodyIterator rbIter;
229      RigidBody* rb;
226 –    
227 –    for (mol = info->beginMolecule(mi); mol != NULL; mol = info->nextMolecule(mi)) {
230  
231 <        for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
232 <            compareProperty(atom, bs, property, comparator, comparisonValue);
233 <        }
234 <        
235 <        //change the positions of atoms which belong to the rigidbodies
236 <        for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
237 <            compareProperty(rb, bs, property, comparator, comparisonValue);
238 <        }        
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 < }
245 >  }
246  
247 < void SelectionEvaluator::compareProperty(StuntDouble* sd, BitSet& bs, int property, int comparator, float comparisonValue) {
248 <        double propertyValue;
249 <        switch (property) {
250 <        case Token::mass:
251 <            propertyValue = sd->getMass();
252 <            break;
253 <        case Token::charge:
254 <            return;
255 <            //break;
256 <        case Token::dipole:
257 <            return;
258 <            //break;
259 <        default:
260 <            unrecognizedAtomProperty(property);
261 <        }
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 < }
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, BitSet& bs){
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);
313 >      distance = boost::any_cast<float>(withinSpec);
314      } else if (withinSpec.type() == typeid(int)) {
315 <        distance = boost::any_cast<int>(withinSpec);    
315 >      distance = boost::any_cast<int>(withinSpec);    
316      } else {
317 <        evalError("casting error in withinInstruction");
318 <        bs.clearAll();
317 >      evalError("casting error in withinInstruction");
318 >      bs.clearAll();
319      }
320      
321      bs = distanceFinder.find(bs, distance);            
322 < }
323 <
324 < void SelectionEvaluator::define() {
322 >  }
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,
330 +                                               expression(statement, 2)));
331 +  }
332 +  
333  
334 <    variables.insert(VariablesType::value_type(variable, expression(statement, 2)));
335 < }
336 <
308 <
309 < /** @todo */
310 < void SelectionEvaluator::predefine(const std::string& script) {
311 <
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 || (tok & Token::predefinedset) == Token::predefinedset) {
348 <                std::string variable = boost::any_cast<std::string>(statement[1].value);
349 <                variables.insert(VariablesType::value_type(variable, statement));
350 <
351 <            } else {
352 <                evalError("invalid variable name:" + script);
353 <            }
354 <        }else {
355 <            evalError("bad predefinition length:" + script);
356 <        }
357 <
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());
360 >      evalError("predefined set compile error:" + script +
361 >                "\ncompile error:" + compiler.getErrorMessage());
362      }
363 +  }
364  
365 < }
340 <
341 < void SelectionEvaluator::select(BitSet& bs){
365 >  void SelectionEvaluator::select(OpenMDBitSet& bs){
366      bs = expression(statement, 1);
367 < }
368 <
369 < BitSet SelectionEvaluator::lookupValue(const std::string& variable){
370 <
371 <    BitSet bs(nStuntDouble);
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(BitSet)) {
376 <            return boost::any_cast<BitSet>(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 <        }
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);
383 >      unrecognizedIdentifier(variable);
384      }
385 <
385 >    
386      return bs;
387 < }
387 >  }
388 >  
389 >  OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){    
390 >    return nameFinder.match(name);    
391 >  }    
392  
393 < BitSet SelectionEvaluator::nameInstruction(const std::string& name){
366 <    
367 <    return nameFinder.match(name);
368 <
369 < }    
370 <
371 < bool SelectionEvaluator::containDynamicToken(const std::vector<Token>& tokens){
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 <        }
396 >      if (i->tok & Token::dynamic) {
397 >        return true;
398 >      }
399      }
400 <
400 >    
401      return false;
402 < }    
402 >  }    
403  
404 < void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
404 >  void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
405      variables.clear();
406      //load predefine
407      //predefine();
408 < }
408 >  }
409  
410 < BitSet SelectionEvaluator::evaluate() {
411 <    BitSet bs(nStuntDouble);
410 >  OpenMDBitSet SelectionEvaluator::evaluate() {
411 >    OpenMDBitSet bs(nStuntDouble);
412      if (isLoaded_) {
413 <        pc = 0;
414 <        instructionDispatchLoop(bs);
413 >      pc = 0;
414 >      instructionDispatchLoop(bs);
415      }
416  
417      return bs;
418 < }
418 >  }
419  
420 < BitSet SelectionEvaluator::indexInstruction(const boost::any& value) {
421 <    BitSet bs(nStuntDouble);
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 <            indexFinder.find(index);
429 <        }
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 <            indexFinder.find(indexRange.first, indexRange.second);
437 <        }
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 < }
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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