| 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).           | 
| 38 | 
> | 
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).           | 
| 39 | 
  | 
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010). | 
| 40 | 
  | 
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). | 
| 41 | 
  | 
 */ | 
| 56 | 
  | 
 | 
| 57 | 
  | 
  SelectionEvaluator::SelectionEvaluator(SimInfo* si)  | 
| 58 | 
  | 
    : info(si), nameFinder(info), distanceFinder(info), hullFinder(info), | 
| 59 | 
< | 
      indexFinder(info),  | 
| 59 | 
> | 
      indexFinder(info), hasSurfaceArea_(false), | 
| 60 | 
  | 
      isLoaded_(false){     | 
| 61 | 
< | 
      nStuntDouble = info->getNGlobalAtoms() + info->getNGlobalRigidBodies(); | 
| 62 | 
< | 
    }             | 
| 63 | 
< | 
 | 
| 61 | 
> | 
    nObjects.push_back(info->getNGlobalAtoms() + info->getNGlobalRigidBodies()); | 
| 62 | 
> | 
    nObjects.push_back(info->getNGlobalBonds()); | 
| 63 | 
> | 
    nObjects.push_back(info->getNGlobalBends()); | 
| 64 | 
> | 
    nObjects.push_back(info->getNGlobalTorsions()); | 
| 65 | 
> | 
    nObjects.push_back(info->getNGlobalInversions()); | 
| 66 | 
> | 
    nObjects.push_back(info->getNGlobalMolecules());     | 
| 67 | 
> | 
  } | 
| 68 | 
> | 
   | 
| 69 | 
  | 
  bool SelectionEvaluator::loadScript(const std::string& filename,  | 
| 70 | 
  | 
                                      const std::string& script) { | 
| 71 | 
  | 
    clearDefinitionsAndLoadPredefined(); | 
| 132 | 
  | 
    return loadScript(filename, script); | 
| 133 | 
  | 
  } | 
| 134 | 
  | 
   | 
| 135 | 
< | 
  void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs){ | 
| 135 | 
> | 
  void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs){ | 
| 136 | 
  | 
     | 
| 137 | 
  | 
    while ( pc < aatoken.size()) { | 
| 138 | 
  | 
      statement = aatoken[pc++]; | 
| 153 | 
  | 
 | 
| 154 | 
  | 
  } | 
| 155 | 
  | 
 | 
| 156 | 
< | 
  void SelectionEvaluator::instructionDispatchLoop(OpenMDBitSet& bs, int frame){ | 
| 156 | 
> | 
  void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs, int frame){ | 
| 157 | 
  | 
     | 
| 158 | 
  | 
    while ( pc < aatoken.size()) { | 
| 159 | 
  | 
      statement = aatoken[pc++]; | 
| 174 | 
  | 
 | 
| 175 | 
  | 
  } | 
| 176 | 
  | 
 | 
| 177 | 
< | 
  OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,  | 
| 177 | 
> | 
  SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,  | 
| 178 | 
  | 
                                             int pcStart) { | 
| 179 | 
< | 
    OpenMDBitSet bs; | 
| 180 | 
< | 
    std::stack<OpenMDBitSet> stack;  | 
| 179 | 
> | 
    SelectionSet bs = createSelectionSets(); | 
| 180 | 
> | 
    std::stack<SelectionSet> stack;  | 
| 181 | 
> | 
    vector<int> bsSize = bs.size(); | 
| 182 | 
  | 
    | 
| 183 | 
  | 
    for (unsigned int pc = pcStart; pc < code.size(); ++pc) { | 
| 184 | 
  | 
      Token instruction = code[pc]; | 
| 190 | 
  | 
        break; | 
| 191 | 
  | 
      case Token::all: | 
| 192 | 
  | 
        bs = allInstruction(); | 
| 193 | 
< | 
        stack.push(bs);             | 
| 193 | 
> | 
        stack.push(bs); | 
| 194 | 
  | 
        break; | 
| 195 | 
  | 
      case Token::none: | 
| 196 | 
< | 
        bs = OpenMDBitSet(nStuntDouble); | 
| 197 | 
< | 
        stack.push(bs);             | 
| 196 | 
> | 
        bs = createSelectionSets(); | 
| 197 | 
> | 
        stack.push(bs); | 
| 198 | 
  | 
        break; | 
| 199 | 
  | 
      case Token::opOr: | 
| 200 | 
< | 
        bs = stack.top(); | 
| 201 | 
< | 
        stack.pop(); | 
| 202 | 
< | 
        stack.top() |= bs; | 
| 200 | 
> | 
          bs= stack.top(); | 
| 201 | 
> | 
          stack.pop(); | 
| 202 | 
> | 
          stack.top() |= bs; | 
| 203 | 
  | 
        break; | 
| 204 | 
  | 
      case Token::opAnd: | 
| 205 | 
< | 
        bs = stack.top(); | 
| 206 | 
< | 
        stack.pop(); | 
| 207 | 
< | 
        stack.top() &= bs; | 
| 205 | 
> | 
          bs = stack.top(); | 
| 206 | 
> | 
          stack.pop(); | 
| 207 | 
> | 
          stack.top() &= bs; | 
| 208 | 
  | 
        break; | 
| 209 | 
  | 
      case Token::opNot: | 
| 210 | 
< | 
        stack.top().flip(); | 
| 210 | 
> | 
          stack.top().flip(); | 
| 211 | 
  | 
        break; | 
| 212 | 
  | 
      case Token::within: | 
| 213 | 
  | 
        withinInstruction(instruction, stack.top()); | 
| 214 | 
  | 
        break; | 
| 215 | 
  | 
      case Token::hull: | 
| 216 | 
< | 
        stack.push(hull()); | 
| 216 | 
> | 
          stack.push(hull()); | 
| 217 | 
  | 
        break; | 
| 218 | 
  | 
        //case Token::selected: | 
| 219 | 
  | 
        //  stack.push(getSelectionSet()); | 
| 220 | 
  | 
        //  break; | 
| 221 | 
  | 
      case Token::name: | 
| 222 | 
< | 
        stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value))); | 
| 222 | 
> | 
          stack.push(nameInstruction(boost::any_cast<std::string>(instruction.value))); | 
| 223 | 
  | 
        break; | 
| 224 | 
  | 
      case Token::index: | 
| 225 | 
< | 
        stack.push(indexInstruction(instruction.value)); | 
| 225 | 
> | 
          stack.push(indexInstruction(instruction.value)); | 
| 226 | 
  | 
        break; | 
| 227 | 
  | 
      case Token::identifier: | 
| 228 | 
< | 
        stack.push(lookupValue(boost::any_cast<std::string>(instruction.value))); | 
| 228 | 
> | 
          stack.push(lookupValue(boost::any_cast<std::string>(instruction.value))); | 
| 229 | 
  | 
        break; | 
| 230 | 
  | 
      case Token::opLT: | 
| 231 | 
  | 
      case Token::opLE: | 
| 246 | 
  | 
  } | 
| 247 | 
  | 
 | 
| 248 | 
  | 
 | 
| 249 | 
< | 
  OpenMDBitSet SelectionEvaluator::expression(const std::vector<Token>& code,  | 
| 249 | 
> | 
  SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,  | 
| 250 | 
  | 
                                              int pcStart, int frame) { | 
| 251 | 
< | 
    OpenMDBitSet bs; | 
| 252 | 
< | 
    std::stack<OpenMDBitSet> stack;  | 
| 251 | 
> | 
    SelectionSet bs = createSelectionSets(); | 
| 252 | 
> | 
    std::stack<SelectionSet> stack;  | 
| 253 | 
  | 
    | 
| 254 | 
  | 
    for (unsigned int pc = pcStart; pc < code.size(); ++pc) { | 
| 255 | 
  | 
      Token instruction = code[pc]; | 
| 264 | 
  | 
        stack.push(bs);             | 
| 265 | 
  | 
        break; | 
| 266 | 
  | 
      case Token::none: | 
| 267 | 
< | 
        bs = OpenMDBitSet(nStuntDouble); | 
| 267 | 
> | 
        bs = SelectionSet(nObjects); | 
| 268 | 
  | 
        stack.push(bs);             | 
| 269 | 
  | 
        break; | 
| 270 | 
  | 
      case Token::opOr: | 
| 318 | 
  | 
 | 
| 319 | 
  | 
 | 
| 320 | 
  | 
 | 
| 321 | 
< | 
  OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { | 
| 321 | 
> | 
  SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction) { | 
| 322 | 
  | 
    int comparator = instruction.tok; | 
| 323 | 
  | 
    int property = instruction.intValue; | 
| 324 | 
  | 
    float comparisonValue = boost::any_cast<float>(instruction.value); | 
| 325 | 
< | 
    OpenMDBitSet bs(nStuntDouble); | 
| 325 | 
> | 
    SelectionSet bs = createSelectionSets(); | 
| 326 | 
  | 
    bs.clearAll(); | 
| 327 | 
  | 
     | 
| 328 | 
  | 
    SimInfo::MoleculeIterator mi; | 
| 335 | 
  | 
    for (mol = info->beginMolecule(mi); mol != NULL;  | 
| 336 | 
  | 
         mol = info->nextMolecule(mi)) { | 
| 337 | 
  | 
 | 
| 338 | 
+ | 
      compareProperty(mol, bs, property, comparator, comparisonValue); | 
| 339 | 
+ | 
 | 
| 340 | 
  | 
      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { | 
| 341 | 
  | 
        compareProperty(atom, bs, property, comparator, comparisonValue); | 
| 342 | 
  | 
      } | 
| 350 | 
  | 
    return bs; | 
| 351 | 
  | 
  } | 
| 352 | 
  | 
 | 
| 353 | 
< | 
  OpenMDBitSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) { | 
| 353 | 
> | 
  SelectionSet SelectionEvaluator::comparatorInstruction(const Token& instruction, int frame) { | 
| 354 | 
  | 
    int comparator = instruction.tok; | 
| 355 | 
  | 
    int property = instruction.intValue; | 
| 356 | 
  | 
    float comparisonValue = boost::any_cast<float>(instruction.value); | 
| 357 | 
< | 
    OpenMDBitSet bs(nStuntDouble); | 
| 357 | 
> | 
    SelectionSet bs = createSelectionSets(); | 
| 358 | 
  | 
    bs.clearAll(); | 
| 359 | 
  | 
     | 
| 360 | 
  | 
    SimInfo::MoleculeIterator mi; | 
| 367 | 
  | 
    for (mol = info->beginMolecule(mi); mol != NULL;  | 
| 368 | 
  | 
         mol = info->nextMolecule(mi)) { | 
| 369 | 
  | 
 | 
| 370 | 
+ | 
      compareProperty(mol, bs, property, comparator, comparisonValue, frame); | 
| 371 | 
+ | 
 | 
| 372 | 
  | 
      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { | 
| 373 | 
  | 
        compareProperty(atom, bs, property, comparator, comparisonValue, frame); | 
| 374 | 
  | 
      } | 
| 382 | 
  | 
    return bs; | 
| 383 | 
  | 
  } | 
| 384 | 
  | 
 | 
| 385 | 
< | 
  void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,  | 
| 385 | 
> | 
  void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,  | 
| 386 | 
  | 
                                           int property, int comparator,  | 
| 387 | 
  | 
                                           float comparisonValue) { | 
| 388 | 
  | 
    RealType propertyValue = 0.0; | 
| 389 | 
+ | 
    Vector3d pos; | 
| 390 | 
+ | 
 | 
| 391 | 
  | 
    switch (property) { | 
| 392 | 
  | 
    case Token::mass: | 
| 393 | 
  | 
      propertyValue = sd->getMass(); | 
| 414 | 
  | 
    case Token::z: | 
| 415 | 
  | 
      propertyValue = sd->getPos().z(); | 
| 416 | 
  | 
      break; | 
| 417 | 
+ | 
    case Token::wrappedX:     | 
| 418 | 
+ | 
      pos = sd->getPos(); | 
| 419 | 
+ | 
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); | 
| 420 | 
+ | 
      propertyValue = pos.x(); | 
| 421 | 
+ | 
      break; | 
| 422 | 
+ | 
    case Token::wrappedY: | 
| 423 | 
+ | 
      pos = sd->getPos(); | 
| 424 | 
+ | 
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); | 
| 425 | 
+ | 
      propertyValue = pos.y(); | 
| 426 | 
+ | 
      break; | 
| 427 | 
+ | 
    case Token::wrappedZ: | 
| 428 | 
+ | 
      pos = sd->getPos(); | 
| 429 | 
+ | 
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); | 
| 430 | 
+ | 
      propertyValue = pos.z(); | 
| 431 | 
+ | 
      break; | 
| 432 | 
  | 
    case Token::r: | 
| 433 | 
  | 
      propertyValue = sd->getPos().length(); | 
| 434 | 
  | 
      break; | 
| 457 | 
  | 
      match = propertyValue != comparisonValue; | 
| 458 | 
  | 
      break; | 
| 459 | 
  | 
    } | 
| 460 | 
+ | 
 | 
| 461 | 
  | 
    if (match)  | 
| 462 | 
< | 
      bs.setBitOn(sd->getGlobalIndex()); | 
| 462 | 
> | 
      bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex()); | 
| 463 | 
  | 
 | 
| 464 | 
  | 
     | 
| 465 | 
  | 
  } | 
| 466 | 
  | 
 | 
| 467 | 
< | 
  void SelectionEvaluator::compareProperty(StuntDouble* sd, OpenMDBitSet& bs,  | 
| 467 | 
> | 
  void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,  | 
| 468 | 
  | 
                                           int property, int comparator,  | 
| 469 | 
+ | 
                                           float comparisonValue) { | 
| 470 | 
+ | 
    RealType propertyValue = 0.0; | 
| 471 | 
+ | 
    Vector3d pos; | 
| 472 | 
+ | 
 | 
| 473 | 
+ | 
    switch (property) { | 
| 474 | 
+ | 
    case Token::mass: | 
| 475 | 
+ | 
      propertyValue = mol->getMass(); | 
| 476 | 
+ | 
      break; | 
| 477 | 
+ | 
    case Token::charge: | 
| 478 | 
+ | 
      { | 
| 479 | 
+ | 
        Molecule::AtomIterator ai; | 
| 480 | 
+ | 
        Atom* atom; | 
| 481 | 
+ | 
        for (atom = mol->beginAtom(ai); atom != NULL; | 
| 482 | 
+ | 
             atom = mol->nextAtom(ai)) { | 
| 483 | 
+ | 
          propertyValue+=  getCharge(atom); | 
| 484 | 
+ | 
        } | 
| 485 | 
+ | 
      } | 
| 486 | 
+ | 
      break; | 
| 487 | 
+ | 
    case Token::x: | 
| 488 | 
+ | 
      propertyValue = mol->getCom().x(); | 
| 489 | 
+ | 
      break; | 
| 490 | 
+ | 
    case Token::y: | 
| 491 | 
+ | 
      propertyValue = mol->getCom().y(); | 
| 492 | 
+ | 
      break; | 
| 493 | 
+ | 
    case Token::z: | 
| 494 | 
+ | 
      propertyValue = mol->getCom().z(); | 
| 495 | 
+ | 
      break; | 
| 496 | 
+ | 
    case Token::wrappedX:     | 
| 497 | 
+ | 
      pos = mol->getCom(); | 
| 498 | 
+ | 
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); | 
| 499 | 
+ | 
      propertyValue = pos.x(); | 
| 500 | 
+ | 
      break; | 
| 501 | 
+ | 
    case Token::wrappedY: | 
| 502 | 
+ | 
      pos = mol->getCom(); | 
| 503 | 
+ | 
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); | 
| 504 | 
+ | 
      propertyValue = pos.y(); | 
| 505 | 
+ | 
      break; | 
| 506 | 
+ | 
    case Token::wrappedZ: | 
| 507 | 
+ | 
      pos = mol->getCom(); | 
| 508 | 
+ | 
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos); | 
| 509 | 
+ | 
      propertyValue = pos.z(); | 
| 510 | 
+ | 
      break; | 
| 511 | 
+ | 
    case Token::r: | 
| 512 | 
+ | 
      propertyValue = mol->getCom().length(); | 
| 513 | 
+ | 
      break; | 
| 514 | 
+ | 
    default: | 
| 515 | 
+ | 
      unrecognizedMoleculeProperty(property); | 
| 516 | 
+ | 
    } | 
| 517 | 
+ | 
     | 
| 518 | 
+ | 
    bool match = false; | 
| 519 | 
+ | 
    switch (comparator) { | 
| 520 | 
+ | 
    case Token::opLT: | 
| 521 | 
+ | 
      match = propertyValue < comparisonValue; | 
| 522 | 
+ | 
      break; | 
| 523 | 
+ | 
    case Token::opLE: | 
| 524 | 
+ | 
      match = propertyValue <= comparisonValue; | 
| 525 | 
+ | 
      break; | 
| 526 | 
+ | 
    case Token::opGE: | 
| 527 | 
+ | 
      match = propertyValue >= comparisonValue; | 
| 528 | 
+ | 
      break; | 
| 529 | 
+ | 
    case Token::opGT: | 
| 530 | 
+ | 
      match = propertyValue > comparisonValue; | 
| 531 | 
+ | 
      break; | 
| 532 | 
+ | 
    case Token::opEQ: | 
| 533 | 
+ | 
      match = propertyValue == comparisonValue; | 
| 534 | 
+ | 
      break; | 
| 535 | 
+ | 
    case Token::opNE: | 
| 536 | 
+ | 
      match = propertyValue != comparisonValue; | 
| 537 | 
+ | 
      break; | 
| 538 | 
+ | 
    } | 
| 539 | 
+ | 
     | 
| 540 | 
+ | 
    if (match)  | 
| 541 | 
+ | 
      bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());     | 
| 542 | 
+ | 
  } | 
| 543 | 
+ | 
 | 
| 544 | 
+ | 
  void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,  | 
| 545 | 
+ | 
                                           int property, int comparator,  | 
| 546 | 
  | 
                                           float comparisonValue, int frame) { | 
| 547 | 
  | 
    RealType propertyValue = 0.0; | 
| 548 | 
+ | 
    Vector3d pos; | 
| 549 | 
  | 
    switch (property) { | 
| 550 | 
  | 
    case Token::mass: | 
| 551 | 
+ | 
      propertyValue = mol->getMass(); | 
| 552 | 
+ | 
      break; | 
| 553 | 
+ | 
    case Token::charge: | 
| 554 | 
+ | 
      { | 
| 555 | 
+ | 
        Molecule::AtomIterator ai; | 
| 556 | 
+ | 
        Atom* atom; | 
| 557 | 
+ | 
        for (atom = mol->beginAtom(ai); atom != NULL; | 
| 558 | 
+ | 
             atom = mol->nextAtom(ai)) { | 
| 559 | 
+ | 
          propertyValue+=  getCharge(atom,frame); | 
| 560 | 
+ | 
        } | 
| 561 | 
+ | 
      }       | 
| 562 | 
+ | 
      break; | 
| 563 | 
+ | 
    case Token::x: | 
| 564 | 
+ | 
      propertyValue = mol->getCom(frame).x(); | 
| 565 | 
+ | 
      break; | 
| 566 | 
+ | 
    case Token::y: | 
| 567 | 
+ | 
      propertyValue = mol->getCom(frame).y(); | 
| 568 | 
+ | 
      break; | 
| 569 | 
+ | 
    case Token::z: | 
| 570 | 
+ | 
      propertyValue = mol->getCom(frame).z(); | 
| 571 | 
+ | 
      break; | 
| 572 | 
+ | 
    case Token::wrappedX:     | 
| 573 | 
+ | 
      pos = mol->getCom(frame); | 
| 574 | 
+ | 
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); | 
| 575 | 
+ | 
      propertyValue = pos.x(); | 
| 576 | 
+ | 
      break; | 
| 577 | 
+ | 
    case Token::wrappedY: | 
| 578 | 
+ | 
      pos = mol->getCom(frame); | 
| 579 | 
+ | 
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); | 
| 580 | 
+ | 
      propertyValue = pos.y(); | 
| 581 | 
+ | 
      break; | 
| 582 | 
+ | 
    case Token::wrappedZ: | 
| 583 | 
+ | 
      pos = mol->getCom(frame); | 
| 584 | 
+ | 
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); | 
| 585 | 
+ | 
      propertyValue = pos.z(); | 
| 586 | 
+ | 
      break; | 
| 587 | 
+ | 
 | 
| 588 | 
+ | 
    case Token::r: | 
| 589 | 
+ | 
      propertyValue = mol->getCom(frame).length(); | 
| 590 | 
+ | 
      break; | 
| 591 | 
+ | 
    default: | 
| 592 | 
+ | 
      unrecognizedMoleculeProperty(property); | 
| 593 | 
+ | 
    } | 
| 594 | 
+ | 
         | 
| 595 | 
+ | 
    bool match = false; | 
| 596 | 
+ | 
    switch (comparator) { | 
| 597 | 
+ | 
    case Token::opLT: | 
| 598 | 
+ | 
      match = propertyValue < comparisonValue; | 
| 599 | 
+ | 
      break; | 
| 600 | 
+ | 
    case Token::opLE: | 
| 601 | 
+ | 
      match = propertyValue <= comparisonValue; | 
| 602 | 
+ | 
      break; | 
| 603 | 
+ | 
    case Token::opGE: | 
| 604 | 
+ | 
      match = propertyValue >= comparisonValue; | 
| 605 | 
+ | 
      break; | 
| 606 | 
+ | 
    case Token::opGT: | 
| 607 | 
+ | 
      match = propertyValue > comparisonValue; | 
| 608 | 
+ | 
      break; | 
| 609 | 
+ | 
    case Token::opEQ: | 
| 610 | 
+ | 
      match = propertyValue == comparisonValue; | 
| 611 | 
+ | 
      break; | 
| 612 | 
+ | 
    case Token::opNE: | 
| 613 | 
+ | 
      match = propertyValue != comparisonValue; | 
| 614 | 
+ | 
      break; | 
| 615 | 
+ | 
    } | 
| 616 | 
+ | 
    if (match)  | 
| 617 | 
+ | 
      bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex()); | 
| 618 | 
+ | 
     | 
| 619 | 
+ | 
     | 
| 620 | 
+ | 
  } | 
| 621 | 
+ | 
  void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,  | 
| 622 | 
+ | 
                                           int property, int comparator,  | 
| 623 | 
+ | 
                                           float comparisonValue, int frame) { | 
| 624 | 
+ | 
    RealType propertyValue = 0.0; | 
| 625 | 
+ | 
    Vector3d pos; | 
| 626 | 
+ | 
    switch (property) { | 
| 627 | 
+ | 
    case Token::mass: | 
| 628 | 
  | 
      propertyValue = sd->getMass(); | 
| 629 | 
  | 
      break; | 
| 630 | 
  | 
    case Token::charge: | 
| 649 | 
  | 
    case Token::z: | 
| 650 | 
  | 
      propertyValue = sd->getPos(frame).z(); | 
| 651 | 
  | 
      break; | 
| 652 | 
+ | 
    case Token::wrappedX:     | 
| 653 | 
+ | 
      pos = sd->getPos(frame); | 
| 654 | 
+ | 
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); | 
| 655 | 
+ | 
      propertyValue = pos.x(); | 
| 656 | 
+ | 
      break; | 
| 657 | 
+ | 
    case Token::wrappedY: | 
| 658 | 
+ | 
      pos = sd->getPos(frame); | 
| 659 | 
+ | 
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); | 
| 660 | 
+ | 
      propertyValue = pos.y(); | 
| 661 | 
+ | 
      break; | 
| 662 | 
+ | 
    case Token::wrappedZ: | 
| 663 | 
+ | 
      pos = sd->getPos(frame); | 
| 664 | 
+ | 
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos); | 
| 665 | 
+ | 
      propertyValue = pos.z(); | 
| 666 | 
+ | 
      break; | 
| 667 | 
+ | 
 | 
| 668 | 
  | 
    case Token::r: | 
| 669 | 
  | 
      propertyValue = sd->getPos(frame).length(); | 
| 670 | 
  | 
      break; | 
| 694 | 
  | 
      break; | 
| 695 | 
  | 
    } | 
| 696 | 
  | 
    if (match)  | 
| 697 | 
< | 
      bs.setBitOn(sd->getGlobalIndex()); | 
| 697 | 
> | 
      bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex()); | 
| 698 | 
  | 
 | 
| 699 | 
  | 
     | 
| 700 | 
  | 
  } | 
| 701 | 
  | 
 | 
| 702 | 
+ | 
   | 
| 703 | 
  | 
  void SelectionEvaluator::withinInstruction(const Token& instruction,  | 
| 704 | 
< | 
                                             OpenMDBitSet& bs){ | 
| 704 | 
> | 
                                             SelectionSet& bs){ | 
| 705 | 
  | 
     | 
| 706 | 
  | 
    boost::any withinSpec = instruction.value; | 
| 707 | 
  | 
    float distance; | 
| 718 | 
  | 
  } | 
| 719 | 
  | 
 | 
| 720 | 
  | 
  void SelectionEvaluator::withinInstruction(const Token& instruction,  | 
| 721 | 
< | 
                                             OpenMDBitSet& bs, int frame){ | 
| 721 | 
> | 
                                             SelectionSet& bs, int frame){ | 
| 722 | 
  | 
     | 
| 723 | 
  | 
    boost::any withinSpec = instruction.value; | 
| 724 | 
  | 
    float distance; | 
| 775 | 
  | 
    } | 
| 776 | 
  | 
  } | 
| 777 | 
  | 
 | 
| 778 | 
< | 
  void SelectionEvaluator::select(OpenMDBitSet& bs){ | 
| 778 | 
> | 
  void SelectionEvaluator::select(SelectionSet& bs){ | 
| 779 | 
  | 
    bs = expression(statement, 1); | 
| 780 | 
  | 
  } | 
| 781 | 
  | 
 | 
| 782 | 
< | 
  void SelectionEvaluator::select(OpenMDBitSet& bs, int frame){ | 
| 782 | 
> | 
  void SelectionEvaluator::select(SelectionSet& bs, int frame){ | 
| 783 | 
  | 
    bs = expression(statement, 1, frame); | 
| 784 | 
  | 
  } | 
| 785 | 
  | 
   | 
| 786 | 
< | 
  OpenMDBitSet SelectionEvaluator::lookupValue(const std::string& variable){ | 
| 786 | 
> | 
  SelectionSet SelectionEvaluator::lookupValue(const std::string& variable){ | 
| 787 | 
  | 
     | 
| 788 | 
< | 
    OpenMDBitSet bs(nStuntDouble); | 
| 788 | 
> | 
    SelectionSet bs = createSelectionSets(); | 
| 789 | 
  | 
    std::map<std::string, boost::any>::iterator i = variables.find(variable); | 
| 790 | 
  | 
     | 
| 791 | 
  | 
    if (i != variables.end()) { | 
| 792 | 
< | 
      if (i->second.type() == typeid(OpenMDBitSet)) { | 
| 793 | 
< | 
        return boost::any_cast<OpenMDBitSet>(i->second); | 
| 792 | 
> | 
      if (i->second.type() == typeid(SelectionSet)) { | 
| 793 | 
> | 
        return boost::any_cast<SelectionSet>(i->second); | 
| 794 | 
  | 
      } else if (i->second.type() ==  typeid(std::vector<Token>)){ | 
| 795 | 
  | 
        bs = expression(boost::any_cast<std::vector<Token> >(i->second), 2); | 
| 796 | 
  | 
        i->second =  bs; /**@todo fixme */ | 
| 803 | 
  | 
    return bs; | 
| 804 | 
  | 
  } | 
| 805 | 
  | 
   | 
| 806 | 
< | 
  OpenMDBitSet SelectionEvaluator::nameInstruction(const std::string& name){     | 
| 806 | 
> | 
  SelectionSet SelectionEvaluator::nameInstruction(const std::string& name){     | 
| 807 | 
  | 
    return nameFinder.match(name);     | 
| 808 | 
  | 
  }     | 
| 809 | 
  | 
 | 
| 824 | 
  | 
    //predefine(); | 
| 825 | 
  | 
  } | 
| 826 | 
  | 
 | 
| 827 | 
< | 
  OpenMDBitSet SelectionEvaluator::evaluate() { | 
| 828 | 
< | 
    OpenMDBitSet bs(nStuntDouble); | 
| 827 | 
> | 
  SelectionSet SelectionEvaluator::createSelectionSets() { | 
| 828 | 
> | 
    SelectionSet ss(nObjects); | 
| 829 | 
> | 
    return ss; | 
| 830 | 
> | 
  } | 
| 831 | 
> | 
 | 
| 832 | 
> | 
  SelectionSet SelectionEvaluator::evaluate() { | 
| 833 | 
> | 
    SelectionSet bs = createSelectionSets(); | 
| 834 | 
  | 
    if (isLoaded_) { | 
| 835 | 
  | 
      pc = 0; | 
| 836 | 
  | 
      instructionDispatchLoop(bs); | 
| 838 | 
  | 
    return bs; | 
| 839 | 
  | 
  } | 
| 840 | 
  | 
 | 
| 841 | 
< | 
  OpenMDBitSet SelectionEvaluator::evaluate(int frame) { | 
| 842 | 
< | 
    OpenMDBitSet bs(nStuntDouble); | 
| 841 | 
> | 
  SelectionSet SelectionEvaluator::evaluate(int frame) { | 
| 842 | 
> | 
    SelectionSet bs = createSelectionSets(); | 
| 843 | 
  | 
    if (isLoaded_) { | 
| 844 | 
  | 
      pc = 0; | 
| 845 | 
  | 
      instructionDispatchLoop(bs, frame); | 
| 847 | 
  | 
    return bs; | 
| 848 | 
  | 
  } | 
| 849 | 
  | 
 | 
| 850 | 
< | 
  OpenMDBitSet SelectionEvaluator::indexInstruction(const boost::any& value) { | 
| 851 | 
< | 
    OpenMDBitSet bs(nStuntDouble); | 
| 850 | 
> | 
  SelectionSet SelectionEvaluator::indexInstruction(const boost::any& value) { | 
| 851 | 
> | 
    SelectionSet bs = createSelectionSets(); | 
| 852 | 
  | 
 | 
| 853 | 
  | 
    if (value.type() == typeid(int)) { | 
| 854 | 
  | 
      int index = boost::any_cast<int>(value); | 
| 855 | 
< | 
      if (index < 0 || index >= bs.size()) { | 
| 855 | 
> | 
      if (index < 0 || index >= bs.bitsets_[STUNTDOUBLE].size()) { | 
| 856 | 
  | 
        invalidIndex(index); | 
| 857 | 
  | 
      } else { | 
| 858 | 
  | 
        bs = indexFinder.find(index); | 
| 860 | 
  | 
    } else if (value.type() == typeid(std::pair<int, int>)) { | 
| 861 | 
  | 
      std::pair<int, int> indexRange= boost::any_cast<std::pair<int, int> >(value); | 
| 862 | 
  | 
      assert(indexRange.first <= indexRange.second); | 
| 863 | 
< | 
      if (indexRange.first < 0 || indexRange.second >= bs.size()) { | 
| 863 | 
> | 
      if (indexRange.first < 0 ||  | 
| 864 | 
> | 
          indexRange.second >= bs.bitsets_[STUNTDOUBLE].size()) { | 
| 865 | 
  | 
        invalidIndexRange(indexRange); | 
| 866 | 
  | 
      }else { | 
| 867 | 
  | 
        bs = indexFinder.find(indexRange.first, indexRange.second); | 
| 871 | 
  | 
    return bs; | 
| 872 | 
  | 
  } | 
| 873 | 
  | 
 | 
| 874 | 
< | 
  OpenMDBitSet SelectionEvaluator::allInstruction() { | 
| 875 | 
< | 
    OpenMDBitSet bs(nStuntDouble); | 
| 874 | 
> | 
  SelectionSet SelectionEvaluator::allInstruction() { | 
| 875 | 
> | 
    SelectionSet ss = createSelectionSets(); | 
| 876 | 
  | 
 | 
| 877 | 
  | 
    SimInfo::MoleculeIterator mi; | 
| 672 | 
– | 
    Molecule* mol; | 
| 878 | 
  | 
    Molecule::AtomIterator ai; | 
| 674 | 
– | 
    Atom* atom; | 
| 879 | 
  | 
    Molecule::RigidBodyIterator rbIter; | 
| 880 | 
+ | 
    Molecule::BondIterator bondIter; | 
| 881 | 
+ | 
    Molecule::BendIterator bendIter; | 
| 882 | 
+ | 
    Molecule::TorsionIterator torsionIter; | 
| 883 | 
+ | 
    Molecule::InversionIterator inversionIter; | 
| 884 | 
+ | 
 | 
| 885 | 
+ | 
    Molecule* mol; | 
| 886 | 
+ | 
    Atom* atom; | 
| 887 | 
  | 
    RigidBody* rb; | 
| 888 | 
+ | 
    Bond* bond; | 
| 889 | 
+ | 
    Bend* bend; | 
| 890 | 
+ | 
    Torsion* torsion; | 
| 891 | 
+ | 
    Inversion* inversion;     | 
| 892 | 
  | 
 | 
| 893 | 
  | 
    // Doing the loop insures that we're actually on this processor. | 
| 894 | 
  | 
 | 
| 895 | 
  | 
    for (mol = info->beginMolecule(mi); mol != NULL;  | 
| 896 | 
  | 
         mol = info->nextMolecule(mi)) { | 
| 682 | 
– | 
 | 
| 897 | 
  | 
      for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { | 
| 898 | 
< | 
        bs.setBitOn(atom->getGlobalIndex()); | 
| 899 | 
< | 
      } | 
| 686 | 
< | 
      | 
| 898 | 
> | 
        ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex()); | 
| 899 | 
> | 
      }      | 
| 900 | 
  | 
      for (rb = mol->beginRigidBody(rbIter); rb != NULL;  | 
| 901 | 
  | 
           rb = mol->nextRigidBody(rbIter)) { | 
| 902 | 
< | 
        bs.setBitOn(rb->getGlobalIndex()); | 
| 902 | 
> | 
        ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex()); | 
| 903 | 
  | 
      } | 
| 904 | 
+ | 
      for (bond = mol->beginBond(bondIter); bond != NULL;  | 
| 905 | 
+ | 
           bond = mol->nextBond(bondIter)) { | 
| 906 | 
+ | 
        ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex()); | 
| 907 | 
+ | 
      }    | 
| 908 | 
+ | 
      for (bend = mol->beginBend(bendIter); bend != NULL;  | 
| 909 | 
+ | 
           bend = mol->nextBend(bendIter)) { | 
| 910 | 
+ | 
        ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex()); | 
| 911 | 
+ | 
      }    | 
| 912 | 
+ | 
      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;  | 
| 913 | 
+ | 
           torsion = mol->nextTorsion(torsionIter)) { | 
| 914 | 
+ | 
        ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex()); | 
| 915 | 
+ | 
      }    | 
| 916 | 
+ | 
      for (inversion = mol->beginInversion(inversionIter); inversion != NULL;  | 
| 917 | 
+ | 
           inversion = mol->nextInversion(inversionIter)) { | 
| 918 | 
+ | 
        ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex()); | 
| 919 | 
+ | 
      } | 
| 920 | 
+ | 
      ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex()); | 
| 921 | 
  | 
    } | 
| 922 | 
  | 
 | 
| 923 | 
< | 
    return bs; | 
| 923 | 
> | 
    return ss; | 
| 924 | 
  | 
  } | 
| 925 | 
  | 
 | 
| 926 | 
< | 
  OpenMDBitSet SelectionEvaluator::hull() { | 
| 927 | 
< | 
    OpenMDBitSet bs(nStuntDouble); | 
| 926 | 
> | 
  SelectionSet SelectionEvaluator::hull() { | 
| 927 | 
> | 
    SelectionSet bs = createSelectionSets(); | 
| 928 | 
  | 
     | 
| 929 | 
  | 
    bs = hullFinder.findHull(); | 
| 930 | 
< | 
     | 
| 930 | 
> | 
    surfaceArea_ = hullFinder.getSurfaceArea(); | 
| 931 | 
> | 
    hasSurfaceArea_ = true; | 
| 932 | 
  | 
    return bs; | 
| 933 | 
  | 
  } | 
| 934 | 
  | 
 | 
| 935 | 
  | 
 | 
| 936 | 
< | 
  OpenMDBitSet SelectionEvaluator::hull(int frame) { | 
| 937 | 
< | 
    OpenMDBitSet bs(nStuntDouble); | 
| 936 | 
> | 
  SelectionSet SelectionEvaluator::hull(int frame) { | 
| 937 | 
> | 
    SelectionSet bs = createSelectionSets(); | 
| 938 | 
  | 
     | 
| 939 | 
  | 
    bs = hullFinder.findHull(frame); | 
| 940 | 
< | 
     | 
| 940 | 
> | 
 | 
| 941 | 
  | 
    return bs; | 
| 942 | 
  | 
  } | 
| 943 | 
  | 
 |