SelectionEvaluator.cpp

/*
 * Copyright (c) 2004-present, The University of Notre Dame. All rights
 * reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright notice,
 *    this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright notice,
 *    this list of conditions and the following disclaimer in the documentation
 *    and/or other materials provided with the distribution.
 *
 * 3. Neither the name of the copyright holder nor the names of its
 *    contributors may be used to endorse or promote products derived from
 *    this software without specific prior written permission.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
 * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
 * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 * POSSIBILITY OF SUCH DAMAGE.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *
 * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
 * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
 * [4] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 * [5] Kuang & Gezelter, Mol. Phys., 110, 691-701 (2012).
 * [6] Lamichhane, Gezelter & Newman, J. Chem. Phys. 141, 134109 (2014).
 * [7] Lamichhane, Newman & Gezelter, J. Chem. Phys. 141, 134110 (2014).
 * [8] Bhattarai, Newman & Gezelter, Phys. Rev. B 99, 094106 (2019).
 */
 
#include "selection/SelectionEvaluator.hpp"
 
#include <any>
#include <map>
#include <stack>
#include <string>
#include <utility>
 
#include "io/ifstrstream.hpp"
#include "primitives/Atom.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "primitives/Molecule.hpp"
#include "primitives/RigidBody.hpp"
#include "types/FixedChargeAdapter.hpp"
#include "types/FluctuatingChargeAdapter.hpp"
 
namespace OpenMD {
 
  SelectionEvaluator::SelectionEvaluator(SimInfo* si) :
      info(si), nameFinder(info), distanceFinder(info), hullFinder(info),
      alphaHullFinder(info), indexFinder(info), isLoaded_(false),
      hasSurfaceArea_(false), hasVolume_(false) {
    nObjects.push_back(info->getNGlobalAtoms() + info->getNGlobalRigidBodies());
    nObjects.push_back(info->getNGlobalBonds());
    nObjects.push_back(info->getNGlobalBends());
    nObjects.push_back(info->getNGlobalTorsions());
    nObjects.push_back(info->getNGlobalInversions());
    nObjects.push_back(info->getNGlobalMolecules());
  }
 
  bool SelectionEvaluator::loadScript(const std::string& filename,
                                      const std::string& script) {
    clearDefinitionsAndLoadPredefined();
    this->filename = filename;
    this->script   = script;
    if (!compiler.compile(filename, script)) {
      error        = true;
      errorMessage = compiler.getErrorMessage();
 
      snprintf(painCave.errMsg, MAX_SIM_ERROR_MSG_LENGTH,
               "SelectionCompiler Error: %s\n", errorMessage.c_str());
      painCave.severity = OPENMD_ERROR;
      painCave.isFatal  = 1;
      simError();
      return false;
    }
 
    pc          = 0;
    aatoken     = compiler.getAatokenCompiled();
    linenumbers = compiler.getLineNumbers();
    lineIndices = compiler.getLineIndices();
 
    std::vector<std::vector<Token>>::const_iterator i;
 
    isDynamic_ = false;
    for (i = aatoken.begin(); i != aatoken.end(); ++i) {
      if (containDynamicToken(*i)) {
        isDynamic_ = true;
        break;
      }
    }
 
    isLoaded_ = true;
    return true;
  }
 
  void SelectionEvaluator::clearState() {
    error        = false;
    errorMessage = "";
  }
 
  bool SelectionEvaluator::loadScriptString(const std::string& script) {
    clearState();
    return loadScript("", script);
  }
 
  bool SelectionEvaluator::loadScriptFile(const std::string& filename) {
    clearState();
    return loadScriptFileInternal(filename);
  }
 
  bool SelectionEvaluator::loadScriptFileInternal(const std::string& filename) {
    ifstrstream ifs(filename.c_str());
    if (!ifs.is_open()) { return false; }
 
    const int bufferSize = 65535;
    char buffer[bufferSize];
    std::string script;
    while (ifs.getline(buffer, bufferSize)) {
      script += buffer;
    }
    return loadScript(filename, script);
  }
 
  void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs) {
    while (pc < aatoken.size()) {
      statement       = aatoken[pc++];
      statementLength = statement.size();
      Token token     = statement[0];
      switch (token.tok) {
      case Token::define:
        define();
        break;
      case Token::select:
        select(bs);
        break;
      default:
        unrecognizedCommand(token);
        return;
      }
    }
  }
 
  void SelectionEvaluator::instructionDispatchLoop(SelectionSet& bs,
                                                   int frame) {
    while (pc < aatoken.size()) {
      statement       = aatoken[pc++];
      statementLength = statement.size();
      Token token     = statement[0];
      switch (token.tok) {
      case Token::define:
        define();
        break;
      case Token::select:
        select(bs, frame);
        break;
      default:
        unrecognizedCommand(token);
        return;
      }
    }
  }
 
  SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
                                              int pcStart) {
    SelectionSet bs = createSelectionSets();
    std::stack<SelectionSet> stack;
    vector<int> bsSize = bs.size();
 
    for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
      Token instruction = code[pc];
 
      switch (instruction.tok) {
      case Token::expressionBegin:
        break;
      case Token::expressionEnd:
        break;
      case Token::all:
        bs = allInstruction();
        stack.push(bs);
        break;
      case Token::none:
        bs = createSelectionSets();
        stack.push(bs);
        break;
      case Token::opOr:
        bs = stack.top();
        stack.pop();
        stack.top() |= bs;
        break;
      case Token::opAnd:
        bs = stack.top();
        stack.pop();
        stack.top() &= bs;
        break;
      case Token::opNot:
        stack.top().flip();
        break;
      case Token::within:
        withinInstruction(instruction, stack.top());
        break;
      case Token::alphahull:
        stack.push(alphaHullInstruction(instruction));
        break;
      case Token::hull:
        stack.push(hull());
        break;
        // case Token::selected:
        //  stack.push(getSelectionSet());
        //  break;
      case Token::name:
        stack.push(
            nameInstruction(std::any_cast<std::string>(instruction.value)));
        break;
      case Token::index:
        stack.push(indexInstruction(instruction.value));
        break;
      case Token::identifier:
        stack.push(lookupValue(std::any_cast<std::string>(instruction.value)));
        break;
      case Token::opLT:
      case Token::opLE:
      case Token::opGE:
      case Token::opGT:
      case Token::opEQ:
      case Token::opNE:
        stack.push(comparatorInstruction(instruction));
        break;
      default:
        unrecognizedExpression();
      }
    }
    if (stack.size() != 1)
      evalError("atom expression compiler error - stack over/underflow");
 
    return stack.top();
  }
 
  SelectionSet SelectionEvaluator::expression(const std::vector<Token>& code,
                                              int pcStart, int frame) {
    SelectionSet bs = createSelectionSets();
    std::stack<SelectionSet> stack;
 
    for (unsigned int pc = pcStart; pc < code.size(); ++pc) {
      Token instruction = code[pc];
 
      switch (instruction.tok) {
      case Token::expressionBegin:
        break;
      case Token::expressionEnd:
        break;
      case Token::all:
        bs = allInstruction();
        stack.push(bs);
        break;
      case Token::none:
        bs = SelectionSet(nObjects);
        stack.push(bs);
        break;
      case Token::opOr:
        bs = stack.top();
        stack.pop();
        stack.top() |= bs;
        break;
      case Token::opAnd:
        bs = stack.top();
        stack.pop();
        stack.top() &= bs;
        break;
      case Token::opNot:
        stack.top().flip();
        break;
      case Token::within:
        withinInstruction(instruction, stack.top(), frame);
        break;
      case Token::alphahull:
        stack.push(alphaHullInstruction(instruction, frame));
        break;
      case Token::hull:
        stack.push(hull(frame));
        break;
        // case Token::selected:
        //  stack.push(getSelectionSet());
        //  break;
      case Token::name:
        stack.push(
            nameInstruction(std::any_cast<std::string>(instruction.value)));
        break;
      case Token::index:
        stack.push(indexInstruction(instruction.value));
        break;
      case Token::identifier:
        stack.push(lookupValue(std::any_cast<std::string>(instruction.value)));
        break;
      case Token::opLT:
      case Token::opLE:
      case Token::opGE:
      case Token::opGT:
      case Token::opEQ:
      case Token::opNE:
        stack.push(comparatorInstruction(instruction, frame));
        break;
      default:
        unrecognizedExpression();
      }
    }
    if (stack.size() != 1)
      evalError("atom expression compiler error - stack over/underflow");
 
    return stack.top();
  }
 
  SelectionSet SelectionEvaluator::comparatorInstruction(
      const Token& instruction) {
    int comparator        = instruction.tok;
    int property          = instruction.intValue;
    float comparisonValue = std::any_cast<float>(instruction.value);
    SelectionSet bs       = createSelectionSets();
    bs.clearAll();
 
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
 
    for (mol = info->beginMolecule(mi); mol != NULL;
         mol = info->nextMolecule(mi)) {
      compareProperty(mol, bs, property, comparator, comparisonValue);
 
      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        compareProperty(atom, bs, property, comparator, comparisonValue);
      }
 
      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
           rb = mol->nextRigidBody(rbIter)) {
        compareProperty(rb, bs, property, comparator, comparisonValue);
      }
    }
 
    return bs.parallelReduce();
  }
 
  SelectionSet SelectionEvaluator::comparatorInstruction(
      const Token& instruction, int frame) {
    int comparator        = instruction.tok;
    int property          = instruction.intValue;
    float comparisonValue = std::any_cast<float>(instruction.value);
    SelectionSet bs       = createSelectionSets();
    bs.clearAll();
 
    SimInfo::MoleculeIterator mi;
    Molecule* mol;
    Molecule::AtomIterator ai;
    Atom* atom;
    Molecule::RigidBodyIterator rbIter;
    RigidBody* rb;
 
    for (mol = info->beginMolecule(mi); mol != NULL;
         mol = info->nextMolecule(mi)) {
      compareProperty(mol, bs, property, comparator, comparisonValue, frame);
 
      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        compareProperty(atom, bs, property, comparator, comparisonValue, frame);
      }
 
      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
           rb = mol->nextRigidBody(rbIter)) {
        compareProperty(rb, bs, property, comparator, comparisonValue, frame);
      }
    }
 
    return bs.parallelReduce();
  }
 
  void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
                                           int property, int comparator,
                                           float comparisonValue) {
    RealType propertyValue = 0.0;
    Vector3d pos;
 
    switch (property) {
    case Token::atomno:
      if (sd->isAtom()) {
        Atom* atom    = static_cast<Atom*>(sd);
        propertyValue = atom->getGlobalIndex();
      }
      break;
    case Token::mass:
      propertyValue = sd->getMass();
      break;
    case Token::charge:
      if (sd->isAtom()) {
        Atom* atom    = static_cast<Atom*>(sd);
        propertyValue = getCharge(atom);
      } else if (sd->isRigidBody()) {
        RigidBody* rb = static_cast<RigidBody*>(sd);
        RigidBody::AtomIterator ai;
        Atom* atom;
        for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
          propertyValue += getCharge(atom);
        }
      }
      break;
    case Token::x:
      propertyValue = sd->getPos().x();
      break;
    case Token::y:
      propertyValue = sd->getPos().y();
      break;
    case Token::z:
      propertyValue = sd->getPos().z();
      break;
    case Token::wrappedX:
      pos = sd->getPos();
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
      propertyValue = pos.x();
      break;
    case Token::wrappedY:
      pos = sd->getPos();
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
      propertyValue = pos.y();
      break;
    case Token::wrappedZ:
      pos = sd->getPos();
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
      propertyValue = pos.z();
      break;
    case Token::r:
      propertyValue = sd->getPos().length();
      break;
    default:
      unrecognizedAtomProperty(property);
    }
 
    bool match = false;
    switch (comparator) {
    case Token::opLT:
      match = propertyValue < comparisonValue;
      break;
    case Token::opLE:
      match = propertyValue <= comparisonValue;
      break;
    case Token::opGE:
      match = propertyValue >= comparisonValue;
      break;
    case Token::opGT:
      match = propertyValue > comparisonValue;
      break;
    case Token::opEQ:
      match = fabs(propertyValue - comparisonValue) <= OpenMD::epsilon;
      break;
    case Token::opNE:
      match = propertyValue != comparisonValue;
      break;
    }
 
    if (match) bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
  }
 
  void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
                                           int property, int comparator,
                                           float comparisonValue) {
    RealType propertyValue = 0.0;
    Vector3d pos;
 
    switch (property) {
    case Token::mass:
      propertyValue = mol->getMass();
      break;
    case Token::charge: {
      Molecule::AtomIterator ai;
      Atom* atom;
      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        propertyValue += getCharge(atom);
      }
    } break;
    case Token::x:
      propertyValue = mol->getCom().x();
      break;
    case Token::y:
      propertyValue = mol->getCom().y();
      break;
    case Token::z:
      propertyValue = mol->getCom().z();
      break;
    case Token::wrappedX:
      pos = mol->getCom();
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
      propertyValue = pos.x();
      break;
    case Token::wrappedY:
      pos = mol->getCom();
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
      propertyValue = pos.y();
      break;
    case Token::wrappedZ:
      pos = mol->getCom();
      info->getSnapshotManager()->getCurrentSnapshot()->wrapVector(pos);
      propertyValue = pos.z();
      break;
    case Token::r:
      propertyValue = mol->getCom().length();
      break;
    default:
      unrecognizedMoleculeProperty(property);
    }
 
    bool match = false;
    switch (comparator) {
    case Token::opLT:
      match = propertyValue < comparisonValue;
      break;
    case Token::opLE:
      match = propertyValue <= comparisonValue;
      break;
    case Token::opGE:
      match = propertyValue >= comparisonValue;
      break;
    case Token::opGT:
      match = propertyValue > comparisonValue;
      break;
    case Token::opEQ:
      match = fabs(propertyValue - comparisonValue) <= OpenMD::epsilon;
      break;
    case Token::opNE:
      match = propertyValue != comparisonValue;
      break;
    }
 
    if (match) bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
  }
 
  void SelectionEvaluator::compareProperty(Molecule* mol, SelectionSet& bs,
                                           int property, int comparator,
                                           float comparisonValue, int frame) {
    RealType propertyValue = 0.0;
    Vector3d pos;
    switch (property) {
    case Token::mass:
      propertyValue = mol->getMass();
      break;
    case Token::charge: {
      Molecule::AtomIterator ai;
      Atom* atom;
      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        propertyValue += getCharge(atom, frame);
      }
    } break;
    case Token::x:
      propertyValue = mol->getCom(frame).x();
      break;
    case Token::y:
      propertyValue = mol->getCom(frame).y();
      break;
    case Token::z:
      propertyValue = mol->getCom(frame).z();
      break;
    case Token::wrappedX:
      pos = mol->getCom(frame);
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
      propertyValue = pos.x();
      break;
    case Token::wrappedY:
      pos = mol->getCom(frame);
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
      propertyValue = pos.y();
      break;
    case Token::wrappedZ:
      pos = mol->getCom(frame);
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
      propertyValue = pos.z();
      break;
 
    case Token::r:
      propertyValue = mol->getCom(frame).length();
      break;
    default:
      unrecognizedMoleculeProperty(property);
    }
 
    bool match = false;
    switch (comparator) {
    case Token::opLT:
      match = propertyValue < comparisonValue;
      break;
    case Token::opLE:
      match = propertyValue <= comparisonValue;
      break;
    case Token::opGE:
      match = propertyValue >= comparisonValue;
      break;
    case Token::opGT:
      match = propertyValue > comparisonValue;
      break;
    case Token::opEQ:
      match = fabs(propertyValue - comparisonValue) <= OpenMD::epsilon;
      break;
    case Token::opNE:
      match = propertyValue != comparisonValue;
      break;
    }
    if (match) bs.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
  }
  void SelectionEvaluator::compareProperty(StuntDouble* sd, SelectionSet& bs,
                                           int property, int comparator,
                                           float comparisonValue, int frame) {
    RealType propertyValue = 0.0;
    Vector3d pos;
    switch (property) {
    case Token::atomno:
      if (sd->isAtom()) {
        Atom* atom    = static_cast<Atom*>(sd);
        propertyValue = atom->getGlobalIndex();
      }
      break;
    case Token::mass:
      propertyValue = sd->getMass();
      break;
    case Token::charge:
      if (sd->isAtom()) {
        Atom* atom    = static_cast<Atom*>(sd);
        propertyValue = getCharge(atom, frame);
      } else if (sd->isRigidBody()) {
        RigidBody* rb = static_cast<RigidBody*>(sd);
        RigidBody::AtomIterator ai;
        Atom* atom;
        for (atom = rb->beginAtom(ai); atom != NULL; atom = rb->nextAtom(ai)) {
          propertyValue += getCharge(atom, frame);
        }
      }
      break;
    case Token::x:
      propertyValue = sd->getPos(frame).x();
      break;
    case Token::y:
      propertyValue = sd->getPos(frame).y();
      break;
    case Token::z:
      propertyValue = sd->getPos(frame).z();
      break;
    case Token::wrappedX:
      pos = sd->getPos(frame);
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
      propertyValue = pos.x();
      break;
    case Token::wrappedY:
      pos = sd->getPos(frame);
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
      propertyValue = pos.y();
      break;
    case Token::wrappedZ:
      pos = sd->getPos(frame);
      info->getSnapshotManager()->getSnapshot(frame)->wrapVector(pos);
      propertyValue = pos.z();
      break;
 
    case Token::r:
      propertyValue = sd->getPos(frame).length();
      break;
    default:
      unrecognizedAtomProperty(property);
    }
 
    bool match = false;
    switch (comparator) {
    case Token::opLT:
      match = propertyValue < comparisonValue;
      break;
    case Token::opLE:
      match = propertyValue <= comparisonValue;
      break;
    case Token::opGE:
      match = propertyValue >= comparisonValue;
      break;
    case Token::opGT:
      match = propertyValue > comparisonValue;
      break;
    case Token::opEQ:
      match = fabs(propertyValue - comparisonValue) <= OpenMD::epsilon;
      break;
    case Token::opNE:
      match = propertyValue != comparisonValue;
      break;
    }
    if (match) bs.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
  }
 
  void SelectionEvaluator::withinInstruction(const Token& instruction,
                                             SelectionSet& bs) {
    std::any withinSpec = instruction.value;
    float distance(0.0);
    if (withinSpec.type() == typeid(float)) {
      distance = std::any_cast<float>(withinSpec);
    } else if (withinSpec.type() == typeid(int)) {
      distance = std::any_cast<int>(withinSpec);
    } else {
      evalError("casting error in withinInstruction");
      bs.clearAll();
    }
 
    bs = distanceFinder.find(bs, distance);
  }
 
  void SelectionEvaluator::withinInstruction(const Token& instruction,
                                             SelectionSet& bs, int frame) {
    std::any withinSpec = instruction.value;
    float distance(0.0);
    if (withinSpec.type() == typeid(float)) {
      distance = std::any_cast<float>(withinSpec);
    } else if (withinSpec.type() == typeid(int)) {
      distance = std::any_cast<int>(withinSpec);
    } else {
      evalError("casting error in withinInstruction");
      bs.clearAll();
    }
 
    bs = distanceFinder.find(bs, distance, frame);
  }
 
  SelectionSet SelectionEvaluator::alphaHullInstruction(
      const Token& instruction) {
    SelectionSet bs = createSelectionSets();
 
    std::any alphaSpec = instruction.value;
    float alpha(0.0);
    if (alphaSpec.type() == typeid(float)) {
      alpha = std::any_cast<float>(alphaSpec);
    } else if (alphaSpec.type() == typeid(int)) {
      alpha = std::any_cast<int>(alphaSpec);
    } else {
      evalError("casting error in alphaHullInstruction");
      bs.clearAll();
    }
 
    alphaHullFinder.setAlpha(alpha);
    bs              = alphaHullFinder.findHull();
    surfaceArea_    = alphaHullFinder.getSurfaceArea();
    hasSurfaceArea_ = true;
    volume_         = alphaHullFinder.getVolume();
    hasVolume_      = true;
 
    return bs.parallelReduce();
  }
 
  SelectionSet SelectionEvaluator::alphaHullInstruction(
      const Token& instruction, int frame) {
    SelectionSet bs = createSelectionSets();
 
    std::any alphaSpec = instruction.value;
    float alpha(0.0);
    if (alphaSpec.type() == typeid(float)) {
      alpha = std::any_cast<float>(alphaSpec);
    } else if (alphaSpec.type() == typeid(int)) {
      alpha = std::any_cast<int>(alphaSpec);
    } else {
      evalError("casting error in alphaHullInstruction");
      bs.clearAll();
    }
 
    alphaHullFinder.setAlpha(alpha);
    bs              = alphaHullFinder.findHull(frame);
    surfaceArea_    = alphaHullFinder.getSurfaceArea();
    hasSurfaceArea_ = true;
    volume_         = alphaHullFinder.getVolume();
    hasVolume_      = true;
 
    return bs.parallelReduce();
  }
 
  void SelectionEvaluator::define() {
    assert(statement.size() >= 3);
 
    std::string variable = std::any_cast<std::string>(statement[1].value);
 
    variables.insert(
        VariablesType::value_type(variable, expression(statement, 2)));
  }
 
  /** @todo */
  void SelectionEvaluator::predefine(const std::string& script) {
    if (compiler.compile("#predefine", script)) {
      std::vector<std::vector<Token>> aatoken = compiler.getAatokenCompiled();
      if (aatoken.size() != 1) {
        evalError("predefinition does not have exactly 1 command:" + script);
        return;
      }
      std::vector<Token> statement = aatoken[0];
      if (statement.size() > 2) {
        int tok = statement[1].tok;
        if (tok == Token::identifier ||
            (tok & Token::predefinedset) == Token::predefinedset) {
          std::string variable = std::any_cast<std::string>(statement[1].value);
          variables.insert(VariablesType::value_type(variable, statement));
 
        } else {
          evalError("invalid variable name:" + script);
        }
      } else {
        evalError("bad predefinition length:" + script);
      }
 
    } else {
      evalError("predefined set compile error:" + script +
                "\ncompile error:" + compiler.getErrorMessage());
    }
  }
 
  void SelectionEvaluator::select(SelectionSet& bs) {
    bs = expression(statement, 1);
  }
 
  void SelectionEvaluator::select(SelectionSet& bs, int frame) {
    bs = expression(statement, 1, frame);
  }
 
  SelectionSet SelectionEvaluator::lookupValue(const std::string& variable) {
    SelectionSet bs                             = createSelectionSets();
    std::map<std::string, std::any>::iterator i = variables.find(variable);
 
    if (i != variables.end()) {
      if (i->second.type() == typeid(SelectionSet)) {
        return std::any_cast<SelectionSet>(i->second);
      } else if (i->second.type() == typeid(std::vector<Token>)) {
        bs        = expression(std::any_cast<std::vector<Token>>(i->second), 2);
        i->second = bs; /**@todo fixme */
        return bs.parallelReduce();
      }
    } else {
      unrecognizedIdentifier(variable);
    }
 
    return bs.parallelReduce();
  }
 
  SelectionSet SelectionEvaluator::nameInstruction(const std::string& name) {
    return nameFinder.match(name);
  }
 
  bool SelectionEvaluator::containDynamicToken(
      const std::vector<Token>& tokens) {
    std::vector<Token>::const_iterator i;
    for (i = tokens.begin(); i != tokens.end(); ++i) {
      if (i->tok & Token::dynamic) { return true; }
    }
 
    return false;
  }
 
  void SelectionEvaluator::clearDefinitionsAndLoadPredefined() {
    variables.clear();
    // load predefine
    // predefine();
  }
 
  SelectionSet SelectionEvaluator::createSelectionSets() {
    SelectionSet ss(nObjects);
    return ss;
  }
 
  SelectionSet SelectionEvaluator::evaluate() {
    SelectionSet bs = createSelectionSets();
    if (isLoaded_) {
      pc = 0;
      instructionDispatchLoop(bs);
    }
    return bs.parallelReduce();
  }
 
  SelectionSet SelectionEvaluator::evaluate(int frame) {
    SelectionSet bs = createSelectionSets();
    if (isLoaded_) {
      pc = 0;
      instructionDispatchLoop(bs, frame);
    }
    return bs.parallelReduce();
  }
 
  SelectionSet SelectionEvaluator::indexInstruction(const std::any& value) {
    SelectionSet bs = createSelectionSets();
 
    if (value.type() == typeid(int)) {
      int index = std::any_cast<int>(value);
      if (index < 0 ||
          index >= static_cast<int>(bs.bitsets_[STUNTDOUBLE].size())) {
        invalidIndex(index);
      } else {
        bs = indexFinder.find(index);
      }
    } else if (value.type() == typeid(std::pair<int, int>)) {
      std::pair<int, int> indexRange =
          std::any_cast<std::pair<int, int>>(value);
      assert(indexRange.first <= indexRange.second);
      if (indexRange.first < 0 ||
          indexRange.second >=
              static_cast<int>(bs.bitsets_[STUNTDOUBLE].size())) {
        invalidIndexRange(indexRange);
      } else {
        bs = indexFinder.find(indexRange.first, indexRange.second);
      }
    }
 
    return bs.parallelReduce();
  }
 
  SelectionSet SelectionEvaluator::allInstruction() {
    SelectionSet ss = createSelectionSets();
 
    SimInfo::MoleculeIterator mi;
    Molecule::AtomIterator ai;
    Molecule::RigidBodyIterator rbIter;
    Molecule::BondIterator bondIter;
    Molecule::BendIterator bendIter;
    Molecule::TorsionIterator torsionIter;
    Molecule::InversionIterator inversionIter;
 
    Molecule* mol;
    Atom* atom;
    RigidBody* rb;
    Bond* bond;
    Bend* bend;
    Torsion* torsion;
    Inversion* inversion;
 
    // Doing the loop insures that we're actually on this processor.
 
    for (mol = info->beginMolecule(mi); mol != NULL;
         mol = info->nextMolecule(mi)) {
      for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
        ss.bitsets_[STUNTDOUBLE].setBitOn(atom->getGlobalIndex());
      }
      for (rb = mol->beginRigidBody(rbIter); rb != NULL;
           rb = mol->nextRigidBody(rbIter)) {
        ss.bitsets_[STUNTDOUBLE].setBitOn(rb->getGlobalIndex());
      }
      for (bond = mol->beginBond(bondIter); bond != NULL;
           bond = mol->nextBond(bondIter)) {
        ss.bitsets_[BOND].setBitOn(bond->getGlobalIndex());
      }
      for (bend = mol->beginBend(bendIter); bend != NULL;
           bend = mol->nextBend(bendIter)) {
        ss.bitsets_[BEND].setBitOn(bend->getGlobalIndex());
      }
      for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
           torsion = mol->nextTorsion(torsionIter)) {
        ss.bitsets_[TORSION].setBitOn(torsion->getGlobalIndex());
      }
      for (inversion = mol->beginInversion(inversionIter); inversion != NULL;
           inversion = mol->nextInversion(inversionIter)) {
        ss.bitsets_[INVERSION].setBitOn(inversion->getGlobalIndex());
      }
      ss.bitsets_[MOLECULE].setBitOn(mol->getGlobalIndex());
    }
 
    return ss;
  }
 
  SelectionSet SelectionEvaluator::hull() {
    SelectionSet bs = createSelectionSets();
 
    bs              = hullFinder.findHull();
    surfaceArea_    = hullFinder.getSurfaceArea();
    hasSurfaceArea_ = true;
    volume_         = hullFinder.getVolume();
    hasVolume_      = true;
 
    return bs.parallelReduce();
  }
 
  SelectionSet SelectionEvaluator::hull(int frame) {
    SelectionSet bs = createSelectionSets();
 
    bs = hullFinder.findHull(frame);
 
    return bs.parallelReduce();
  }
 
  RealType SelectionEvaluator::getCharge(Atom* atom) {
    RealType charge    = 0.0;
    AtomType* atomType = atom->getAtomType();
 
    FixedChargeAdapter fca = FixedChargeAdapter(atomType);
    if (fca.isFixedCharge()) { charge = fca.getCharge(); }
 
    FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
    if (fqa.isFluctuatingCharge()) { charge += atom->getFlucQPos(); }
    return charge;
  }
 
  RealType SelectionEvaluator::getCharge(Atom* atom, int frame) {
    RealType charge    = 0.0;
    AtomType* atomType = atom->getAtomType();
 
    FixedChargeAdapter fca = FixedChargeAdapter(atomType);
    if (fca.isFixedCharge()) { charge = fca.getCharge(); }
 
    FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atomType);
    if (fqa.isFluctuatingCharge()) { charge += atom->getFlucQPos(frame); }
    return charge;
  }
}  // namespace OpenMD