ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/trunk/src/selection/SelectionEvaluator.cpp
(Generate patch)

Comparing trunk/src/selection/SelectionEvaluator.cpp (file contents):
Revision 1364 by cli2, Wed Oct 7 20:49:50 2009 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 47 | Line 47
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),
54 >    : info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
55 >      indexFinder(info),
56        isLoaded_(false){    
57        nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies();
58      }            
# Line 67 | Line 68 | namespace oopse {
68  
69        sprintf( painCave.errMsg,
70                 "SelectionCompiler Error: %s\n", errorMessage.c_str());
71 <      painCave.severity = OOPSE_ERROR;
71 >      painCave.severity = OPENMD_ERROR;
72        painCave.isFatal = 1;
73        simError();
74        return false;
# Line 122 | Line 123 | namespace oopse {
123      return loadScript(filename, script);
124    }
125    
126 <  void SelectionEvaluator::instructionDispatchLoop(OOPSEBitSet& bs){
126 >  void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){
127      
128      while ( pc < aatoken.size()) {
129        statement = aatoken[pc++];
# Line 143 | Line 144 | namespace oopse {
144  
145    }
146  
147 <  OOPSEBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
147 >  OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,
148                                               int pcStart) {
149 <    OOPSEBitSet bs;
150 <    std::stack<OOPSEBitSet> stack;
149 >    OpenMDBitSet bs;
150 >    std::stack<OpenMDBitSet> stack;
151    
152      for (int pc = pcStart; pc < code.size(); ++pc) {
153        Token instruction = code[pc];
# Line 157 | 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 180 | Line 181 | namespace oopse {
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());
# Line 213 | 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 244 | Line 248 | namespace oopse {
248      return bs;
249    }
250  
251 <  void SelectionEvaluator::compareProperty(StuntDouble* sd, OOPSEBitSet& bs,
251 >  void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,
252                                             int property, int comparator,
253                                             float comparisonValue) {
254      RealType propertyValue = 0.0;
# Line 305 | Line 309 | namespace oopse {
309    }
310  
311    void SelectionEvaluator::withinInstruction(const Token& instruction,
312 <                                             OOPSEBitSet& bs){
312 >                                             OpenMDBitSet& bs){
313      
314      boost::any withinSpec = instruction.value;
315      float distance;
# Line 362 | Line 366 | namespace oopse {
366      }
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){
373 >  OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){
374      
375 <    OOPSEBitSet bs(nStuntDouble);
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 386 | Line 390 | namespace oopse {
390      return bs;
391    }
392    
393 <  OOPSEBitSet SelectionEvaluator::nameInstruction(const std::string& name){    
393 >  OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){    
394      return nameFinder.match(name);    
395    }    
396  
# Line 407 | 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 417 | 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 441 | Line 445 | namespace oopse {
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();
# Line 455 | 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          }

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines