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root/OpenMD/trunk/src/selection/SelectionEvaluator.cpp
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Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 282 by tim, Thu Feb 3 14:04:59 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 < bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
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 <        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;
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 < }
93 >  }
94  
95 < void SelectionEvaluator::clearState() {
63 <    for (int i = scriptLevelMax; --i >= 0; )
64 <        stack[i].clear();
65 <    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  string & filename) {
111 <
112 < }
113 <
114 < void SelectionEvaluator::instructionDispatchLoop(){
115 <
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();
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      }
102 – }
143  
144 <  BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
105 <    int numberOfAtoms = viewer.getAtomCount();
106 <    BitSet bs;
107 <    BitSet[] stack = new BitSet[10];
108 <    int sp = 0;
144 >  }
145  
146 <    for (int pc = pcStart; ; ++pc) {
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) {
# Line 116 | Line 157 | void SelectionEvaluator::instructionDispatchLoop(){
157        case Token::expressionEnd:
158          break;
159        case Token::all:
160 <        bs = stack[sp++] = new BitSet(numberOfAtoms);
161 <        for (int i = numberOfAtoms; --i >= 0; )
162 <          bs.set(i);
160 >        bs = OpenMDBitSet(nStuntDouble);
161 >        bs.setAll();
162 >        stack.push(bs);            
163          break;
164        case Token::none:
165 <        stack[sp++] = new BitSet();
165 >        bs = OpenMDBitSet(nStuntDouble);
166 >        stack.push(bs);            
167          break;
168        case Token::opOr:
169 <        bs = stack[--sp];
170 <        stack[sp-1].or(bs);
169 >        bs = stack.top();
170 >        stack.pop();
171 >        stack.top() |= bs;
172          break;
173        case Token::opAnd:
174 <        bs = stack[--sp];
175 <        stack[sp-1].and(bs);
174 >        bs = stack.top();
175 >        stack.pop();
176 >        stack.top() &= bs;
177          break;
178        case Token::opNot:
179 <        bs = stack[sp - 1];
136 <        notSet(bs);
179 >        stack.top().flip();
180          break;
181        case Token::within:
182 <        bs = stack[sp - 1];
140 <        stack[sp - 1] = new BitSet();
141 <        withinInstruction(instruction, bs, stack[sp - 1]);
182 >        withinInstruction(instruction, stack.top());
183          break;
184 <      case Token::selected:
185 <        stack[sp++] = copyBitSet(viewer.getSelectionSet());
186 <        break;
184 >        //case Token::selected:
185 >        //  stack.push(getSelectionSet());
186 >        //  break;
187        case Token::name:
188 <
188 >        stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
189          break;
190 <      case  Token::index:
191 <        
190 >      case Token::index:
191 >        stack.push(indexInstruction(instruction.value));
192          break;
152 –      case Token::molname:  
153 –
154 –        break;
155 –      case Token::molindex:
156 –        break;
193        case Token::identifier:
194 <        stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
194 >        stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
195          break;
196        case Token::opLT:
197        case Token::opLE:
# Line 163 | Line 199 | void SelectionEvaluator::instructionDispatchLoop(){
199        case Token::opGT:
200        case Token::opEQ:
201        case Token::opNE:
202 <        bs = stack[sp++] = new BitSet();
167 <        comparatorInstruction(instruction, bs);
202 >        stack.push(comparatorInstruction(instruction));
203          break;
204        default:
205          unrecognizedExpression();
206        }
207      }
208 <    if (sp != 1)
208 >    if (stack.size() != 1)
209        evalError("atom expression compiler error - stack over/underflow");
210 <    return stack[0];
210 >          
211 >    return stack.top();
212    }
213  
214  
215  
216 <  void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
216 >  OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
217      int comparator = instruction.tok;
218      int property = instruction.intValue;
219 <    float propertyValue = 0; // just for temperature
220 <    int comparisonValue = ((Integer)instruction.value).intValue();
221 <    int numberOfAtoms = viewer.getAtomCount();
222 <    Frame frame = viewer.getFrame();
223 <    for (int i = 0; i < numberOfAtoms; ++i) {
224 <      Atom atom = frame.getAtomAt(i);
225 <      switch (property) {
226 <      case Token::mass:
227 <        //propertyValue = atom.getAtomNumber();
228 <        break;
229 <      case Token::charge:
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 <        break;
232 <      case Token::dipole:
231 >    for (mol = info->beginMolecule(mi); mol != NULL;
232 >         mol = info->nextMolecule(mi)) {
233  
234 <        break;
235 <      default:
200 <        unrecognizedAtomProperty(property);
234 >      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
235 >        compareProperty(atom, bs, property, comparator, comparisonValue);
236        }
237 <      bool match = false;
238 <      switch (comparator) {
239 <      case Token::opLT:
240 <        match = propertyValue < comparisonValue;
206 <        break;
207 <      case Token::opLE:
208 <        match = propertyValue <= comparisonValue;
209 <        break;
210 <      case Token::opGE:
211 <        match = propertyValue >= comparisonValue;
212 <        break;
213 <      case Token::opGT:
214 <        match = propertyValue > comparisonValue;
215 <        break;
216 <      case Token::opEQ:
217 <        match = propertyValue == comparisonValue;
218 <        break;
219 <      case Token::opNE:
220 <        match = propertyValue != comparisonValue;
221 <        break;
237 >    
238 >      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
239 >           rb = mol->nextRigidBody(rbIter)) {
240 >        compareProperty(rb, bs, property, comparator, comparisonValue);
241        }
223 –      if (match)
224 –        bs.set(i);
242      }
243 +
244 +    return bs;
245    }
246  
247 < void SelectionEvaluator::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
248 <
249 <    boost::any withinSpec = instruction.value;
250 <    if (withinSpec.type() == typeid(float)){
251 <        withinDistance(boost::any_cast<float>(withinSpec), bs, bsResult);
252 <        return;
253 <    }
254 <    
255 <    evalError("Unrecognized within parameter:" + withinSpec);
256 < }
257 <
258 <  void SelectionEvaluator::withinDistance(float distance, const BitSet& bs, const BitSet& bsResult) {
259 <    Frame frame = viewer.getFrame();
260 <    for (int i = frame.getAtomCount(); --i >= 0; ) {
261 <      if (bs.get(i)) {
262 <        Atom atom = frame.getAtomAt(i);
263 <        AtomIterator iterWithin =
264 <          frame.getWithinIterator(atom, distance);
265 <        while (iterWithin.hasNext())
247 <          bsResult.set(iterWithin.next().getAtomIndex());
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 <
326 >    
327      std::string variable = boost::any_cast<std::string>(statement[1].value);
328      
329 <    variables.insert(std::make_pair(variable, expression(statement, 2)));
329 >    variables.insert(VariablesType::value_type(variable,
330 >                                               expression(statement, 2)));
331    }
332 < }
332 >  
333  
334 < /** @todo */
335 < void SelectionEvaluator::predefine(const std::string& script) {
336 <
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 = (std::string)statement[1].value;
349 <                variables.insert(std::make_pair(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 < }
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 < void SelectionEvaluator::select(){
394 <    viewer.setSelectionSet(expression(statement, 1));
395 < }
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 < BitSet SelectionEvaluator::lookupValue(const std::string& variable){
404 >  void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
405 >    variables.clear();
406 >    //load predefine
407 >    //predefine();
408 >  }
409  
410 <    std::map<std::string, boost::any>::iterator i = variables.find(variable);
410 >  OpenMDBitSet SelectionEvaluator::evaluate() {
411 >    OpenMDBitSet bs(nStuntDouble);
412 >    if (isLoaded_) {
413 >      pc = 0;
414 >      instructionDispatchLoop(bs);
415 >    }
416  
417 <    if (i != variables.end()) {
418 <        if (i->second.type() == typeid(BitSet)) {
419 <            return boost::any_cast<BitSet>(i->second);
420 <        } else if (i->second.type() ==  typeid(std::vector<Token>)){
421 <            BitSet bs = expression(boost::any_cast(i->second), 2);
422 <            i->second =  bs; /**@todo fixme */
423 <            return bs;
424 <        }
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 < }
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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