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root/OpenMD/trunk/src/selection/SelectionEvaluator.cpp
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Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 281 by tim, Wed Feb 2 23:13:11 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 < bool SelectionEvaluator::loadScript(const std::string& filename, const std::string& script) {
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 <        return false;
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 < }
94 >  }
95  
96 < void SelectionEvaluator::clearState() {
63 <    for (int i = scriptLevelMax; --i >= 0; )
64 <        stack[i].clear();
65 <    scriptLevel = 0;
96 >  void SelectionEvaluator::clearState() {
97      error = false;
98      errorMessage = "";
99 < }
99 >  }
100  
101 < bool SelectionEvaluator::loadScriptString(const std::string& script) {
101 >  bool SelectionEvaluator::loadScriptString(const std::string& script) {
102      clearState();
103      return loadScript("", script);
104 < }
104 >  }
105  
106 < bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
106 >  bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
107      clearState();
108      return loadScriptFileInternal(filename);
109 < }
109 >  }
110  
111 <
112 < void SelectionEvaluator::instructionDispatchLoop(){
113 <
114 <    while ( pc < aatoken.size()) {
84 <        statement = aatoken[pc++];
85 <        statementLength = statement.size();
86 <        Token token = statement[0];
87 <        switch (token.tok) {
88 <            case Token::define:
89 <                define();
90 <            break;
91 <            case Token::select:
92 <                select();
93 <            break;
94 <            default:
95 <                unrecognizedCommand(token);
96 <            return;
97 <        }
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 <
118 <  void SelectionEvaluator::predefine(const std::string& script) {
119 <    if (compiler.compile("#predefine", script)) {
120 <      std::vector<std::vector<Token> > aatoken = compiler.getAatokenCompiled();
121 <      if (aatoken.size() != 1) {
122 <        viewer.scriptStatus("predefinition does not have exactly 1 command:"
123 <                            + script);
124 <        return;
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        }
109 –
110 –      std::vector<Token> statement = aatoken[0];
111 –
112 –      if (statement.size() > 2) {
113 –        int tok = statement[1].tok;
114 –        if (tok == Token::identifier ||
115 –            (tok & Token::predefinedset) == Token::predefinedset) {
116 –          std::string variable = (std::string)statement[1].value;
117 –          variables.put(variable, statement);
118 –        } else {
119 –          viewer.scriptStatus("invalid variable name:" + script);
120 –        }
121 –      } else {
122 –        viewer.scriptStatus("bad predefinition length:" + script);
123 –      }
124 –    } else {
125 –      viewer.scriptStatus("predefined set compile error:" + script +
126 –                          "\ncompile error:" + compiler.getErrorMessage());
143      }
144 +
145    }
146  
147 <
148 <
149 <  BitSet SelectionEvaluator::expression(std::vector<Token>& code, int pcStart) {
150 <    int numberOfAtoms = viewer.getAtomCount();
151 <    BitSet bs;
152 <    BitSet[] stack = new BitSet[10];
136 <    int sp = 0;
137 <
138 <    for (int pc = pcStart; ; ++pc) {
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 <      if (logMessages)
141 <        viewer.scriptStatus("instruction=" + instruction);
154 >
155        switch (instruction.tok) {
156        case Token::expressionBegin:
157          break;
158        case Token::expressionEnd:
159 <        break expression_loop;
159 >        break;
160        case Token::all:
161 <        bs = stack[sp++] = new BitSet(numberOfAtoms);
162 <        for (int i = numberOfAtoms; --i >= 0; )
163 <          bs.set(i);
161 >        bs = OpenMDBitSet(nStuntDouble);
162 >        bs.setAll();
163 >        stack.push(bs);            
164          break;
165        case Token::none:
166 <        stack[sp++] = new BitSet();
166 >        bs = OpenMDBitSet(nStuntDouble);
167 >        stack.push(bs);            
168          break;
169        case Token::opOr:
170 <        bs = stack[--sp];
171 <        stack[sp-1].or(bs);
170 >        bs = stack.top();
171 >        stack.pop();
172 >        stack.top() |= bs;
173          break;
174        case Token::opAnd:
175 <        bs = stack[--sp];
176 <        stack[sp-1].and(bs);
175 >        bs = stack.top();
176 >        stack.pop();
177 >        stack.top() &= bs;
178          break;
179        case Token::opNot:
180 <        bs = stack[sp - 1];
165 <        notSet(bs);
180 >        stack.top().flip();
181          break;
182        case Token::within:
183 <        bs = stack[sp - 1];
169 <        stack[sp - 1] = new BitSet();
170 <        withinInstruction(instruction, bs, stack[sp - 1]);
183 >        withinInstruction(instruction, stack.top());
184          break;
185 <      case Token::selected:
186 <        stack[sp++] = copyBitSet(viewer.getSelectionSet());
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 <
192 >        stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value)));
193          break;
194 <      case  Token::index:
195 <        
194 >      case Token::index:
195 >        stack.push(indexInstruction(instruction.value));
196          break;
181 –      case Token::molname:  
182 –
183 –        break;
184 –      case Token::molindex:
185 –        break;
197        case Token::identifier:
198 <        stack[sp++] = lookupIdentifierValue((std::string)instruction.value);
198 >        stack.push(lookupValue(boost::any_cast<std::string>(instruction.value)));
199          break;
200        case Token::opLT:
201        case Token::opLE:
# Line 192 | Line 203 | void SelectionEvaluator::instructionDispatchLoop(){
203        case Token::opGT:
204        case Token::opEQ:
205        case Token::opNE:
206 <        bs = stack[sp++] = new BitSet();
196 <        comparatorInstruction(instruction, bs);
206 >        stack.push(comparatorInstruction(instruction));
207          break;
208        default:
209          unrecognizedExpression();
210        }
211      }
212 <    if (sp != 1)
212 >    if (stack.size() != 1)
213        evalError("atom expression compiler error - stack over/underflow");
214 <    return stack[0];
214 >          
215 >    return stack.top();
216    }
217  
218  
219  
220 <  void SelectionEvaluator::comparatorInstruction(Token instruction, BitSet bs) {
220 >  OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) {
221      int comparator = instruction.tok;
222      int property = instruction.intValue;
223 <    float propertyValue = 0; // just for temperature
224 <    int comparisonValue = ((Integer)instruction.value).intValue();
225 <    int numberOfAtoms = viewer.getAtomCount();
226 <    Frame frame = viewer.getFrame();
227 <    for (int i = 0; i < numberOfAtoms; ++i) {
228 <      Atom atom = frame.getAtomAt(i);
229 <      switch (property) {
230 <      case Token::mass:
231 <        //propertyValue = atom.getAtomNumber();
232 <        break;
233 <      case Token::charge:
234 <
235 <        break;
236 <      case Token::dipole:
237 <
238 <        break;
239 <      default:
240 <        unrecognizedAtomProperty(property);
241 <      }
242 <      bool match = false;
243 <      switch (comparator) {
244 <      case Token::opLT:
245 <        match = propertyValue < comparisonValue;
235 <        break;
236 <      case Token::opLE:
237 <        match = propertyValue <= comparisonValue;
238 <        break;
239 <      case Token::opGE:
240 <        match = propertyValue >= comparisonValue;
241 <        break;
242 <      case Token::opGT:
243 <        match = propertyValue > comparisonValue;
244 <        break;
245 <      case Token::opEQ:
246 <        match = propertyValue == comparisonValue;
247 <        break;
248 <      case Token::opNE:
249 <        match = propertyValue != comparisonValue;
250 <        break;
251 <      }
252 <      if (match)
253 <        bs.set(i);
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::withinInstruction(const Token& instruction, BitSet& bs, BitSet& bsResult)
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 <    if (withinSpec instanceof Float) {
316 <        withinDistance(((Float)withinSpec).floatValue(), bs, bsResult);
317 <        return;
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 <    evalError("Unrecognized within parameter:" + withinSpec);
325 < }
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 <  void SelectionEvaluator::withinDistance(float distance, BitSet bs, BitSet bsResult) {
339 <    Frame frame = viewer.getFrame();
340 <    for (int i = frame.getAtomCount(); --i >= 0; ) {
341 <      if (bs.get(i)) {
342 <        Atom atom = frame.getAtomAt(i);
343 <        AtomIterator iterWithin =
344 <          frame.getWithinIterator(atom, distance);
345 <        while (iterWithin.hasNext())
346 <          bsResult.set(iterWithin.next().getAtomIndex());
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::define() {
370 <    std::string variable = (std::string)statement[1].value;
282 <    variables.insert(std::make_pair(variable, expression(statement, 2)));
369 >  void SelectionEvaluator::select(OpenMDBitSet& bs){
370 >    bs = expression(statement, 1);
371    }
372 < }
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 <  void SelectionEvaluator::predefine(Token[] statement) {
398 <    std::string variable = (std::string)statement[1].value;
399 <    variables.put(variable, statement);
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 <  void SelectionEvaluator::select(){
415 <      viewer.setSelectionSet(expression(statement, 1));
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 <  }
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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