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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 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>
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), hullFinder(info),
55 >      indexFinder(info),
56 >      isLoaded_(false){    
57 >      nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
58 >    }            
59 >
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 >
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 >
77 >    pc = 0;
78 >    aatoken = compiler.getAatokenCompiled();
79 >    linenumbers = compiler.getLineNumbers();
80 >    lineIndices = compiler.getLineIndices();
81 >
82 >    std::vector<std::vector<Token> >::const_iterator i;  
83 >
84 >    isDynamic_ = false;
85 >    for (i = aatoken.begin(); i != aatoken.end(); ++i) {
86 >      if (containDynamicToken(*i)) {
87 >        isDynamic_ = true;
88 >        break;
89 >      }
90 >    }
91 >
92 >    isLoaded_ = true;
93 >    return true;
94 >  }
95 >
96 >  void SelectionEvaluator::clearState() {
97 >    error = false;
98 >    errorMessage = "";
99 >  }
100 >
101 >  bool SelectionEvaluator::loadScriptString(const std::string& script) {
102 >    clearState();
103 >    return loadScript("", script);
104 >  }
105 >
106 >  bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
107 >    clearState();
108 >    return loadScriptFileInternal(filename);
109 >  }
110 >
111 >  bool SelectionEvaluator::loadScriptFileInternal(const std::string & filename) {
112 >    ifstrstream ifs(filename.c_str());
113 >    if (!ifs.is_open()) {
114 >      return false;
115 >    }
116 >    
117 >    const int bufferSize = 65535;
118 >    char buffer[bufferSize];
119 >    std::string script;
120 >    while(ifs.getline(buffer, bufferSize)) {
121 >      script += buffer;
122 >    }
123 >    return loadScript(filename, script);
124 >  }
125 >  
126 >  void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
127 >    
128 >    while ( pc < aatoken.size()) {
129 >      statement = aatoken[pc++];
130 >      statementLength = statement.size();
131 >      Token token = statement[0];
132 >      switch (token.tok) {
133 >      case Token::define:
134 >        define();
135 >        break;
136 >      case Token::select:
137 >        select(bs);
138 >        break;
139 >      default:
140 >        unrecognizedCommand(token);
141 >        return;
142 >      }
143 >    }
144 >
145 >  }
146 >
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 >
155 >      switch (instruction.tok) {
156 >      case Token::expressionBegin:
157 >        break;
158 >      case Token::expressionEnd:
159 >        break;
160 >      case Token::all:
161 >        bs = OpenMDBitSet(nStuntDouble);
162 >        bs.setAll();
163 >        stack.push(bs);            
164 >        break;
165 >      case Token::none:
166 >        bs = OpenMDBitSet(nStuntDouble);
167 >        stack.push(bs);            
168 >        break;
169 >      case Token::opOr:
170 >        bs = stack.top();
171 >        stack.pop();
172 >        stack.top() |= bs;
173 >        break;
174 >      case Token::opAnd:
175 >        bs = stack.top();
176 >        stack.pop();
177 >        stack.top() &= bs;
178 >        break;
179 >      case Token::opNot:
180 >        stack.top().flip();
181 >        break;
182 >      case Token::within:
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;
191 >      case Token::name:
192 >        stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
193 >        break;
194 >      case Token::index:
195 >        stack.push(indexInstruction(instruction.value));
196 >        break;
197 >      case Token::identifier:
198 >        stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
199 >        break;
200 >      case Token::opLT:
201 >      case Token::opLE:
202 >      case Token::opGE:
203 >      case Token::opGT:
204 >      case Token::opEQ:
205 >      case Token::opNE:
206 >        stack.push(comparatorInstruction(instruction));
207 >        break;
208 >      default:
209 >        unrecognizedExpression();
210 >      }
211 >    }
212 >    if (stack.size() != 1)
213 >      evalError("atom expression compiler error - stack over/underflow");
214 >          
215 >    return stack.top();
216 >  }
217 >
218 >
219 >
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 >    OpenMDBitSet bs(nStuntDouble);
226 >    bs.clearAll();
227 >    
228 >    SimInfo::MoleculeIterator mi;
229 >    Molecule* mol;
230 >    Molecule::AtomIterator ai;
231 >    Atom* atom;
232 >    Molecule::RigidBodyIterator rbIter;
233 >    RigidBody* rb;
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;
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, 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();
258 >      break;
259 >    case Token::charge:
260 >      if (sd->isAtom()){
261 >        Atom* atom = static_cast<Atom*>(sd);
262 >        propertyValue = getCharge(atom);
263 >      } else if (sd->isRigidBody()) {
264 >        RigidBody* rb = static_cast<RigidBody*>(sd);
265 >        RigidBody::AtomIterator ai;
266 >        Atom* atom;
267 >        for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
268 >          propertyValue+=  getCharge(atom);
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 >    }
284 >        
285 >    bool match = false;
286 >    switch (comparator) {
287 >    case Token::opLT:
288 >      match = propertyValue < comparisonValue;
289 >      break;
290 >    case Token::opLE:
291 >      match = propertyValue <= comparisonValue;
292 >      break;
293 >    case Token::opGE:
294 >      match = propertyValue >= comparisonValue;
295 >      break;
296 >    case Token::opGT:
297 >      match = propertyValue > comparisonValue;
298 >      break;
299 >    case Token::opEQ:
300 >      match = propertyValue == comparisonValue;
301 >      break;
302 >    case Token::opNE:
303 >      match = propertyValue != comparisonValue;
304 >      break;
305 >    }
306 >    if (match)
307 >      bs.setBitOn(sd->getGlobalIndex());
308 >    
309 >  }
310  
311 +  void SelectionEvaluator::withinInstruction(const Token& instruction,
312 +                                             OpenMDBitSet& bs){
313 +    
314 +    boost::any withinSpec = instruction.value;
315 +    float distance;
316 +    if (withinSpec.type() == typeid(float)){
317 +      distance = boost::any_cast<float>(withinSpec);
318 +    } else if (withinSpec.type() == typeid(int)) {
319 +      distance = boost::any_cast<int>(withinSpec);    
320 +    } else {
321 +      evalError("casting error in withinInstruction");
322 +      bs.clearAll();
323 +    }
324 +    
325 +    bs = distanceFinder.find(bs, distance);            
326 +  }
327 +  
328 +  void SelectionEvaluator::define() {
329 +    assert(statement.size() >= 3);
330 +    
331 +    std::string variable = boost::any_cast<std::string>(statement[1].value);
332 +    
333 +    variables.insert(VariablesType::value_type(variable,
334 +                                               expression(statement, 2)));
335 +  }
336 +  
337  
338 +  /** @todo */
339 +  void SelectionEvaluator::predefine(const std::string& script) {
340 +    
341 +    if (compiler.compile("#predefine", script)) {
342 +      std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
343 +      if (aatoken.size() != 1) {
344 +        evalError("predefinition does not have exactly 1 command:"
345 +                  + script);
346 +        return;
347 +      }
348 +      std::vector<Token> statement = aatoken[0];
349 +      if (statement.size() > 2) {
350 +        int tok = statement[1].tok;
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 +          
356 +        } else {
357 +          evalError("invalid variable name:" + script);
358 +        }
359 +      }else {
360 +        evalError("bad predefinition length:" + script);
361 +      }      
362 +        
363 +    } else {
364 +      evalError("predefined set compile error:" + script +
365 +                "\ncompile error:" + compiler.getErrorMessage());
366 +    }
367 +  }
368 +
369 +  void SelectionEvaluator::select(OpenMDBitSet& bs){
370 +    bs = expression(statement, 1);
371 +  }
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(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 */
384 +        return bs;
385 +      }
386 +    } else {
387 +      unrecognizedIdentifier(variable);
388 +    }
389 +    
390 +    return bs;
391 +  }
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){
398 +    std::vector<Token>::const_iterator i;
399 +    for (i = tokens.begin(); i != tokens.end(); ++i) {
400 +      if (i->tok & Token::dynamic) {
401 +        return true;
402 +      }
403 +    }
404 +    
405 +    return false;
406 +  }    
407 +
408 +  void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
409 +    variables.clear();
410 +    //load predefine
411 +    //predefine();
412 +  }
413 +
414 +  OpenMDBitSet SelectionEvaluator::evaluate() {
415 +    OpenMDBitSet bs(nStuntDouble);
416 +    if (isLoaded_) {
417 +      pc = 0;
418 +      instructionDispatchLoop(bs);
419 +    }
420 +
421 +    return bs;
422 +  }
423 +
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);
429 +      if (index < 0 || index >= bs.size()) {
430 +        invalidIndex(index);
431 +      } else {
432 +        bs = indexFinder.find(index);
433 +      }
434 +    } else if (value.type() == typeid(std::pair<int, int>)) {
435 +      std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value);
436 +      assert(indexRange.first <= indexRange.second);
437 +      if (indexRange.first < 0 || indexRange.second >= bs.size()) {
438 +        invalidIndexRange(indexRange);
439 +      }else {
440 +        bs = indexFinder.find(indexRange.first, indexRange.second);
441 +      }
442 +    }
443 +
444 +    return bs;
445 +  }
446 +
447 +
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");
463 +      if (data != NULL) {
464 +        DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
465 +
466 +        if (doubleData != NULL) {
467 +          charge = doubleData->getData();
468 +
469 +        } else {
470 +          sprintf( painCave.errMsg,
471 +                   "Can not cast GenericData to DoubleGenericData\n");
472 +          painCave.severity = OPENMD_ERROR;
473 +          painCave.isFatal = 1;
474 +          simError();          
475 +        }
476 +      }
477 +    }
478 +
479 +    return charge;
480 +  }
481 +
482   }

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