/* 
   * Build the PairList.
   */ 
   void MdPairPotential::buildPairList() 
   {

      // Recalculate the grid for the internal CellList
      pairList_.makeGrid(boundary());

      // Clear all atoms from the internal CellList
      pairList_.clear();

      // Add every atom in this System to the CellList
      System::MoleculeIterator molIter;
      Molecule::AtomIterator   atomIter;
      for (int iSpec=0; iSpec < simulation().nSpecies(); ++iSpec) {
         for (begin(iSpec, molIter); molIter.notEnd(); ++molIter) {
            molIter->begin(atomIter); 
            for ( ; atomIter.notEnd(); ++atomIter) {
               #ifdef MCMD_SHIFT
               boundary().shift(atomIter->position(), atomIter->shift());
               #else
               boundary().shift(atomIter->position());
               #endif
               pairList_.addAtom(*atomIter);
            }
         }
      }

      // Use the completed CellList to build the PairList 
      pairList_.build(boundary());
   }
   /*
   * Pop and process the next molecule on the workStack (private).
   */
   void ClusterIdentifier::processNextMolecule(Cluster& cluster)
   {
      CellList::NeighborArray neighborArray;
      Molecule::AtomIterator atomIter;
      ClusterLink* thisLinkPtr;
      ClusterLink* otherLinkPtr;
      Atom* otherAtomPtr;
      Boundary& boundary = system().boundary();
      double cutoffSq = cutoff_*cutoff_;
      double rsq;
      int thisMolId, otherMolId, otherClusterId;

      // Pop this molecule off the stack
      thisLinkPtr = &workStack_.pop();
      thisMolId = thisLinkPtr->molecule().id();
      if (thisLinkPtr->clusterId() != cluster.id()) {
         UTIL_THROW("Top ClusterLink not marked with this cluster id");
      }

      /*
      * Loop over atoms of this molecule.
      * For each atom of type atomTypeId_, find neighboring molecules.
      * Add each new neighbor to the cluster, and to the workStack.
      */
      thisLinkPtr->molecule().begin(atomIter); 
      for ( ; atomIter.notEnd(); ++atomIter) {
         if (atomIter->typeId() == atomTypeId_) {
            cellList_.getNeighbors(atomIter->position(), neighborArray);
            for (int i = 0; i < neighborArray.size(); i++) {
               otherAtomPtr = neighborArray[i];
               otherMolId = otherAtomPtr->molecule().id();
               if (otherMolId != thisMolId) {
                  rsq = boundary.distanceSq(atomIter->position(),
                                            otherAtomPtr->position());
                  if (rsq < cutoffSq) {
                     otherLinkPtr = &(links_[otherMolId]);
                     assert(&otherLinkPtr->molecule() ==
                            &otherAtomPtr->molecule());
                     otherClusterId = otherLinkPtr->clusterId();
                     if (otherClusterId == -1) {
                        cluster.addLink(*otherLinkPtr);
                        workStack_.push(*otherLinkPtr);
                     } else
                     if (otherClusterId != cluster.id()) {
                        UTIL_THROW("Cluster Clash!");
                     }
                  }
               }
            } // neighbor atoms
         }
      } // atoms

   }
   /*
   * Evaluate external energy, and add to ensemble. 
   */
   void McExternalEnergyAverage::sample(long iStep) 
   {
      if (!isAtInterval(iStep)) return;

      double energy = 0.0;
      System::MoleculeIterator molIter;
      Molecule::AtomIterator atomIter;
      for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
         for (system().begin(iSpec, molIter); molIter.notEnd(); ++molIter){
             for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
                 energy += system().externalPotential().energy(atomIter->position(), atomIter->typeId());
             }
         }
      }
      accumulator_.sample(energy, outputFile_);
   }
   /* 
   * Build the CellList.
   */ 
   void McPairPotential::buildCellList() 
   {
      // Set up a grid of empty cells.
      cellList_.setup(boundary(), maxPairCutoff());

      // Add all atoms to cellList_ 
      System::MoleculeIterator molIter;
      Molecule::AtomIterator atomIter;
      for (int iSpec=0; iSpec < simulation().nSpecies(); ++iSpec) {
         for (begin(iSpec, molIter); molIter.notEnd(); ++molIter) {
            for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
               boundary().shift(atomIter->position());
               cellList_.addAtom(*atomIter);
            }
         }
      }

   }
   /*
   * Identify all clusters in the system.
   */
   void ClusterIdentifier::identifyClusters()
   {

      // Initialize all data structures:
      // Setup a grid of empty cells
      cellList_.setup(system().boundary(), cutoff_);
      // Clear clusters array and all links
      clusters_.clear();
      for (int i = 0; i < links_.capacity(); ++i) {
         links_[i].clear();
      }

      // Build the cellList, associate Molecule with ClusterLink.
      // Iterate over molecules of species speciesId_
      System::MoleculeIterator molIter;
      Molecule::AtomIterator atomIter;
      system().begin(speciesId_, molIter);
      for ( ; molIter.notEnd(); ++molIter) {

         // Associate this Molecule with a ClusterLink
         links_[molIter->id()].setMolecule(*molIter.get());

         // Add atoms of type = atomTypeId_ to the CellList
         for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
            if (atomIter->typeId() == atomTypeId_) {
               system().boundary().shift(atomIter->position());
               cellList_.addAtom(*atomIter);
            }

         }
      }

      // Identify all clusters
      Cluster* clusterPtr;
      ClusterLink* linkPtr;
      int clusterId = 0;
      system().begin(speciesId_, molIter);
      for ( ; molIter.notEnd(); ++molIter) {

         // Find the link with same index as this molecule
         linkPtr = &(links_[molIter->id()]);
         assert (&(linkPtr->molecule()) == molIter.get());

         // If this link is not in a cluster, begin a new cluster
         if (linkPtr->clusterId() == -1) {

            // Add a new empty cluster to clusters_ array
            clusters_.resize(clusterId+1);
            clusterPtr = &clusters_[clusterId];
            clusterPtr->clear();
            clusterPtr->setId(clusterId);

            // Identify molecules in this cluster
            clusterPtr->addLink(*linkPtr);
            workStack_.push(*linkPtr);
            while (workStack_.size() > 0) {
               processNextMolecule(*clusterPtr);
            }

            clusterId++;
         }

      }

      // Validity check - throws exception on failure.
      isValid();
   }
   /*
   * Verlet MD NVE integrator step
   *
   * This method implements the algorithm:
   *
   *        vm(n)  = v(n) + 0.5*a(n)*dt
   *        x(n+1) = x(n) + vm(n)*dt
   *
   *        calculate acceleration a(n+1)
   *
   *        v(n+1) = vm(n) + 0.5*a(n+1)*dt
   *
   * where x is position, v is velocity, and a is acceleration.
   */
   void NveVvIntegrator::step() 
   {
      Vector dv;
      Vector dr;
      System::MoleculeIterator molIter;
      double prefactor;
      int iSpecies, nSpecies;

      nSpecies = simulation().nSpecies();

      // 1st half velocity Verlet, loop over atoms 
      #if USE_ITERATOR
      Molecule::AtomIterator atomIter;
      for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
         system().begin(iSpecies, molIter); 
         for ( ; molIter.notEnd(); ++molIter) {
            for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {

               prefactor = prefactors_[atomIter->typeId()];

               dv.multiply(atomIter->force(), prefactor);
               atomIter->velocity() += dv;

               dr.multiply(atomIter->velocity(), dt_);
               atomIter->position() += dr;

            }
         }
      }
      #else 
      Atom* atomPtr;
      int   ia;
      for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
         system().begin(iSpecies, molIter); 
         for ( ; molIter.notEnd(); ++molIter) {
            for (ia=0; ia < molIter->nAtom(); ++ia) {
               atomPtr = &molIter->atom(ia);
               prefactor = prefactors_[atomPtr->typeId()];

               dv.multiply(atomPtr->force(), prefactor);
               atomPtr->velocity() += dv;
               dr.multiply(atomPtr->velocity(), dt_);
               
               atomPtr->position() += dr;

            }
         }
      }
      #endif

      system().calculateForces();

      // 2nd half velocity Verlet, loop over atoms
      #if USE_ITERATOR
      for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
         system().begin(iSpecies, molIter); 
         for ( ; molIter.notEnd(); ++molIter) {
            for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
               prefactor = prefactors_[atomIter->typeId()];
               dv.multiply(atomIter->force(), prefactor);
               atomIter->velocity() += dv;
            }
         }
      }
      #else
      for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
         system().begin(iSpecies, molIter); 
         for ( ; molIter.notEnd(); ++molIter)
         {
            for (ia=0; ia < molIter->nAtom(); ++ia) {
               atomPtr = &molIter->atom(ia);
               prefactor = prefactors_[atomPtr->typeId()];
               dv.multiply(atomPtr->force(), prefactor);
               atomPtr->velocity() += dv;
            }
         }
      }
      #endif

      #ifndef INTER_NOPAIR
      if (!system().pairPotential().isPairListCurrent()) {
         system().pairPotential().buildPairList();
      }
      #endif

   }
   /*
   * Generate, attempt and accept or reject a Hybrid MD/MC move.
   */
   bool HybridNphMdMove::move()
   {
      System::MoleculeIterator molIter;
      Molecule::AtomIterator   atomIter;
      double oldEnergy, newEnergy;
      int    iSpec;
      int    nSpec = simulation().nSpecies();

      bool   accept;

      if (nphIntegratorPtr_ == NULL) {
         UTIL_THROW("null integrator pointer");
      }
      // Increment counter for attempted moves
      incrementNAttempt();
      
      // Store old boundary lengths.
      Vector oldLengths = system().boundary().lengths();

      // Store old atom positions in oldPositions_ array.
      for (iSpec = 0; iSpec < nSpec; ++iSpec) {
         mdSystemPtr_->begin(iSpec, molIter);
         for ( ; molIter.notEnd(); ++molIter) {
            for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
               oldPositions_[atomIter->id()] = atomIter->position();
            }
         }
      }

      // Initialize MdSystem
      #ifndef INTER_NOPAIR
      mdSystemPtr_->pairPotential().buildPairList();
      #endif
      mdSystemPtr_->calculateForces();
      mdSystemPtr_->setBoltzmannVelocities(energyEnsemble().temperature());
      nphIntegratorPtr_->setup();
      
      // generate integrator variables from a Gaussian distribution
      Random& random = simulation().random();
      
      double temp = system().energyEnsemble().temperature();
       
      double volume = system().boundary().volume();
      
      if (mode_ == Cubic) {
         // one degree of freedom
	 // barostat_energy = 1/2 (1/W) eta_x^2
         double sigma = sqrt(temp/barostatMass_);
         nphIntegratorPtr_->setEta(0, sigma*random.gaussian());
      } else if (mode_ == Tetragonal) {
         // two degrees of freedom
         // barostat_energy = 1/2 (1/W) eta_x^2 + 1/2 (1/(2W)) eta_y^2
         double sigma1 = sqrt(temp/barostatMass_);
         nphIntegratorPtr_->setEta(0, sigma1*random.gaussian());
         double sigma2 = sqrt(temp/barostatMass_/2.0);
         nphIntegratorPtr_->setEta(1, sigma2*random.gaussian());
      } else if (mode_ == Orthorhombic) { 
         // three degrees of freedom 
         // barostat_energy = 1/2 (1/W) (eta_x^2 + eta_y^2 + eta_z^2)
         double sigma = sqrt(temp/barostatMass_);
         nphIntegratorPtr_->setEta(0, sigma*random.gaussian());
         nphIntegratorPtr_->setEta(1, sigma*random.gaussian());
         nphIntegratorPtr_->setEta(2, sigma*random.gaussian());
      }

      // Store old energy
      oldEnergy  = mdSystemPtr_->potentialEnergy();
      oldEnergy += mdSystemPtr_->kineticEnergy();
      oldEnergy += system().boundaryEnsemble().pressure()*volume;
      oldEnergy += nphIntegratorPtr_->barostatEnergy();

      // Run a short MD simulation
      for (int iStep = 0; iStep < nStep_; ++iStep) {
         nphIntegratorPtr_->step();
      }
      
      volume = system().boundary().volume();

      // Calculate new energy
      newEnergy  = mdSystemPtr_->potentialEnergy();
      newEnergy += mdSystemPtr_->kineticEnergy();
      newEnergy += system().boundaryEnsemble().pressure()*volume;
      newEnergy += nphIntegratorPtr_->barostatEnergy();

      // Decide whether to accept or reject
      accept = random.metropolis( boltzmann(newEnergy-oldEnergy) );

      // Accept move
      if (accept) {
         
         #ifndef INTER_NOPAIR
         // Rebuild the McSystem cellList using the new positions.
         system().pairPotential().buildCellList();
         #endif

         // Increment counter for the number of accepted moves.
         incrementNAccept();

      } else {
         
         // Restore old boundary lengths
         system().boundary().setOrthorhombic(oldLengths);

         // Restore old atom positions
         for (iSpec = 0; iSpec < nSpec; ++iSpec) {
            mdSystemPtr_->begin(iSpec, molIter);
            for ( ; molIter.notEnd(); ++molIter) {
               molIter->begin(atomIter);
               for ( ; atomIter.notEnd(); ++atomIter) {
                  atomIter->position() = oldPositions_[atomIter->id()];
               }
            }
         }

      }

      return accept;

   }
Exemple #8
0
   /**
   * Generate random molecules
   */
   void Linear::generateMolecules(int nMolecule, 
      DArray<double> exclusionRadius, System& system,
      BondPotential *bondPotentialPtr, const Boundary &boundary)
   {
      int iMol;

      // Set up a cell list with twice the maxium exclusion radius as the
      // cell size
      double maxExclusionRadius = 0.0;
      for (int iType = 0; iType < system.simulation().nAtomType(); iType++) {
         if (exclusionRadius[iType] > maxExclusionRadius)
            maxExclusionRadius = exclusionRadius[iType];
      }

      // the minimum cell size is twice the maxExclusionRadius,
      // but to save memory, we take 2 times that value 
      CellList cellList;
      cellList.allocate(system.simulation().atomCapacity(),
         boundary, 2.0*2.0*maxExclusionRadius);

      if (nMolecule > capacity())
         UTIL_THROW("nMolecule > Species.capacity()!"); 

      Simulation& sim = system.simulation();
      for (iMol = 0; iMol < nMolecule; ++iMol) {
         // Add a new molecule to the system
         Molecule &newMolecule= sim.getMolecule(id());
         system.addMolecule(newMolecule);

         // Try placing atoms
         bool moleculeHasBeenPlaced = false;
         for (int iAttempt = 0; iAttempt< maxPlacementAttempts_; iAttempt++) {
            // Place first atom
            Vector pos;
            system.boundary().randomPosition(system.simulation().random(),pos);
            Atom &thisAtom = newMolecule.atom(0);
 
            // check if the first atom can be placed at the new position
            CellList::NeighborArray neighbors;
            cellList.getNeighbors(pos, neighbors);
            int nNeighbor = neighbors.size();
            bool canBePlaced = true;
            for (int j = 0; j < nNeighbor; ++j) {
               Atom *jAtomPtr = neighbors[j];
         
               double r = sqrt(system.boundary().distanceSq(
                                        jAtomPtr->position(), pos));
               if (r < (exclusionRadius[thisAtom.typeId()] +
                  exclusionRadius[jAtomPtr->typeId()])) {
                  canBePlaced = false;
                  break;
               }
            } 
            if (canBePlaced)  {
               thisAtom.position() = pos;
               cellList.addAtom(thisAtom);

               // Try to recursively place other atoms
               if (tryPlaceAtom(newMolecule, 0, exclusionRadius, system,
                  cellList, bondPotentialPtr, system.boundary())) {
                  moleculeHasBeenPlaced = true;
                  break;
              } else {
                 cellList.deleteAtom(thisAtom); 
              }
            }
         }
         if (! moleculeHasBeenPlaced) {
           std::ostringstream oss;
           oss <<  "Failed to place molecule " << newMolecule.id();
           UTIL_THROW(oss.str().c_str());
         }

      }

      #if 0
      // Check
      for (int iMol =0; iMol < nMolecule; ++iMol) {
         Molecule::AtomIterator atomIter;
         system.molecule(id(),iMol).begin(atomIter);
         for (; atomIter.notEnd(); ++atomIter) {
            for (int jMol =0; jMol < nMolecule; ++jMol) {
               Molecule::AtomIterator atomIter2;
               system.molecule(id(),jMol).begin(atomIter2);
               for (; atomIter2.notEnd(); ++atomIter2 ) {
                  if (atomIter2->id() != atomIter->id()) {
                     double r = sqrt(boundary.distanceSq(
                        atomIter->position(),atomIter2->position()));
                     if (r < (exclusionRadius[atomIter->typeId()]+
                        exclusionRadius[atomIter2->typeId()])) {
                        std::cout << r << std::endl;
                        UTIL_THROW("ERROR");
                     }
                  }
               }
            }
         }
      }
      #endif

   } 
   /*
   * Nose-Hoover integrator step.
   *
   * This implements a reversible Velocity-Verlet MD NVT integrator step.
   *
   * Reference: Winkler, Kraus, and Reineker, J. Chem. Phys. 102, 9018 (1995).
   */
   void NvtNhIntegrator::step() 
   {
      Vector  dv;
      Vector  dr;
      System::MoleculeIterator molIter;
      double  dtHalf = 0.5*dt_;
      double  prefactor;
      double  factor;
      Molecule::AtomIterator atomIter;
      int  iSpecies, nSpecies;
      int  nAtom;

      T_target_ = energyEnsemblePtr_->temperature();
      nSpecies  = simulation().nSpecies();
      nAtom     = system().nAtom();

      factor = exp(-dtHalf*(xi_ + xiDot_*dtHalf));

      // 1st half velocity Verlet, loop over atoms 
      for (iSpecies = 0; iSpecies < nSpecies; ++iSpecies) {
         system().begin(iSpecies, molIter); 
         for ( ; molIter.notEnd(); ++molIter) {

            molIter->begin(atomIter); 
            for ( ; atomIter.notEnd(); ++atomIter) {

               atomIter->velocity() *= factor;

               prefactor = prefactors_[atomIter->typeId()];
               dv.multiply(atomIter->force(), prefactor);
               //dv.multiply(atomIter->force(), dtHalf);

               atomIter->velocity() += dv;
               dr.multiply(atomIter->velocity(), dt_);

               atomIter->position() += dr;

            }

         }
      }

      // First half of update of xi_
      xi_ += xiDot_*dtHalf;

      #ifndef INTER_NOPAIR
      // Rebuild the pair list if necessary
      if (!system().pairPotential().isPairListCurrent()) {
         system().pairPotential().buildPairList();
      }
      #endif

      system().calculateForces();

      // 2nd half velocity Verlet, loop over atoms
      for (iSpecies=0; iSpecies < nSpecies; ++iSpecies) {
         system().begin(iSpecies, molIter); 
         for ( ; molIter.notEnd(); ++molIter) {
            for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
               prefactor = prefactors_[atomIter->typeId()];
               dv.multiply(atomIter->force(), prefactor);
               atomIter->velocity() += dv;
               atomIter->velocity() *=factor;
            }
         }
      }

      // Update xiDot and complete update of xi_
      T_kinetic_ = system().kineticEnergy()*2.0/double(3*nAtom);
      xiDot_ = (T_kinetic_/T_target_ -1.0)*nuT_*nuT_;
      xi_ += xiDot_*dtHalf;

   }
Exemple #10
0
   /*
   * Perform replica exchange move.
   */
   bool ReplicaMove::move()
   {
      MPI::Request request[4];
      MPI::Status  status;
      System::MoleculeIterator molIter;
      Molecule::AtomIterator   atomIter;
      int iA;
      int recvPt, sendPt;
  
      DArray<int> permutation;
      permutation.allocate(nProcs_);

      // Gather all derivatives of the perturbation Hamiltonians and parameters on processor with rank 0
      DArray<double> myDerivatives;
      myDerivatives.allocate(nParameters_);
      DArray<double> myParameters;
      myParameters.allocate(nParameters_);

      for (int i=0; i< nParameters_; i++) {
         myDerivatives[i] = system().perturbation().derivative(i);
         myParameters[i] = system().perturbation().parameter(i);
      }

      int size = 0;
      size += memorySize(myDerivatives);
      size += memorySize(myParameters);

      if (myId_ != 0) {

         MemoryOArchive sendCurrent;
         sendCurrent.allocate(size);

         sendCurrent << myDerivatives;
         sendCurrent << myParameters;

         sendCurrent.send(*communicatorPtr_, 0);
      } else {
         DArray< DArray<double> > allDerivatives;
         DArray< DArray<double> > allParameters;
         allDerivatives.allocate(nProcs_);
         allParameters.allocate(nProcs_);
   
         allDerivatives[0].allocate(nParameters_);
         allDerivatives[0] = myDerivatives;
         allParameters[0].allocate(nParameters_);
         allParameters[0] = myParameters;

         for (int i = 1; i<nProcs_; i++) {
            MemoryIArchive recvPartner;
            recvPartner.allocate(size);
            recvPartner.recv(*communicatorPtr_, i);
            allDerivatives[i].allocate(nParameters_);
            allParameters[i].allocate(nParameters_);
            recvPartner >> allDerivatives[i];
            recvPartner >> allParameters[i];
         }

         // Now we have the complete matrix U_ij = u_i(x_j), permutate nsampling steps according
         // to acceptance criterium
  
         // start with identity permutation
         for (int i = 0; i < nProcs_; i++)
            permutation[i] = i;

         for (int n =0; n < nSampling_; n++) {
            swapAttempt_++;
            // choose a pair i,j, i!= j at random
            int i = system().simulation().random().uniformInt(0,nProcs_);
            int j = system().simulation().random().uniformInt(0,nProcs_-1);
            if (i<=j) j++;

            // apply acceptance criterium
            double weight = 0;
            for (int k = 0; k < nParameters_; k++) {
               double deltaDerivative = allDerivatives[i][k] - allDerivatives[j][k];
               // the permutations operate on the states (the perturbation parameters)
               weight += (allParameters[permutation[j]][k] - allParameters[permutation[i]][k])*deltaDerivative;
             }
            double exponential = exp(-weight);
            int accept = system().simulation().random(). metropolis(exponential) ? 1 : 0;
   
            if (accept) {
               swapAccept_++;
               // swap states of pair i,j
               int tmp = permutation[i];
               permutation[i] = permutation[j];
               permutation[j] = tmp;
               }
         }
    
         // send exchange partner information to all other processors
         for (int i = 0; i < nProcs_; i++) {
            if (i != 0)
                communicatorPtr_->Send(&permutation[i], 1, MPI::INT, i, 0);
            else
                sendPt = permutation[i];

            if (permutation[i] != 0)
               communicatorPtr_->Send(&i, 1, MPI::INT, permutation[i], 1);
            else
               recvPt = i;
         }
      }

      
      if (myId_ != 0) {
         // partner id to receive from
         communicatorPtr_->Recv(&sendPt, 1, MPI::INT, 0, 0);
         // partner id to send to
         communicatorPtr_->Recv(&recvPt, 1, MPI::INT, 0, 1);
      }

      if (recvPt == myId_ || sendPt == myId_) {
         // no exchange necessary
         outputFile_ << sendPt << std::endl;
         return true;
      }

      assert(recvPt != myId_ && sendPt != myId_);

      Vector myBoundary;
      myBoundary = system().boundary().lengths();
            
      Vector ptBoundary;
            
      // Accomodate new boundary dimensions.
      request[0] = communicatorPtr_->Irecv(&ptBoundary, 1,
                                           MpiTraits<Vector>::type, recvPt, 1);

      // Send old boundary dimensions.
      request[1] = communicatorPtr_->Isend(&myBoundary, 1,
                                            MpiTraits<Vector>::type, sendPt, 1);

      request[0].Wait();
      request[1].Wait();
             
      system().boundary().setOrthorhombic(ptBoundary);

      // Pack atomic positions and types.
      iA = 0;
      for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
         for (system().begin(iSpec, molIter); molIter.notEnd(); ++molIter){
            for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
               myPositionPtr_[iA] = atomIter->position();
               iA++;
            }
         }
      }
      
      // Accomodate new configuration.
      request[2] = communicatorPtr_->Irecv(ptPositionPtr_, iA,
                       MpiTraits<Vector>::type, recvPt, 2); 

      // Send old configuration.
      request[3] = communicatorPtr_->Isend(myPositionPtr_, iA,
                       MpiTraits<Vector>::type, sendPt, 2);

      request[2].Wait();
      request[3].Wait();
      
      // Adopt the new atomic positions.
      iA = 0;
      for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
         for (system().begin(iSpec, molIter); molIter.notEnd(); ++molIter){
            for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter){
               atomIter->position() = ptPositionPtr_[iA];
               ++iA;
            }
         }
      }
      

      // Notify component observers.
      sendRecvPair partners;
      partners[0] = sendPt;
      partners[1] = recvPt;
      Notifier<sendRecvPair>::notifyObservers(partners);

      // Log information about exchange partner to file
      outputFile_ << sendPt << std::endl;

      return true;

   }
   /*
   * Generate, attempt and accept or reject a Hybrid MD/MC move.
   */
   bool HoomdMove::move()
   {
      if ((!HoomdIsInitialized_) || moleculeSetHasChanged_) {
         initSimulation();
         moleculeSetHasChanged_ = false;
      }

      // We need to create the Integrator every time since we are starting
      // with new coordinates, velocities etc.
      // this does not seem to incur a significant performance decrease
      createIntegrator();

      System::MoleculeIterator molIter;
      Molecule::AtomIterator   atomIter;
      int nSpec = simulation().nSpecies();

      // Increment counter for attempted moves
      incrementNAttempt();

      double oldEnergy, newEnergy;

      {
      // Copy atom coordinates into HOOMD
      ArrayHandle<Scalar4> h_pos(particleDataSPtr_->getPositions(), access_location::host, access_mode::readwrite);
      ArrayHandle<Scalar4> h_vel(particleDataSPtr_->getVelocities(), access_location::host, access_mode::readwrite);
      ArrayHandle<unsigned int> h_tag(particleDataSPtr_->getTags(), access_location::host, access_mode::readwrite);
      ArrayHandle<unsigned int> h_rtag(particleDataSPtr_->getRTags(), access_location::host, access_mode::readwrite);

      for (int iSpec =0; iSpec < nSpec; ++iSpec) {
         system().begin(iSpec, molIter);
         for ( ; molIter.notEnd(); ++ molIter) {
            for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
               unsigned int idx = (unsigned int) atomIter->id();
               Vector& pos = atomIter->position();
               h_pos.data[idx].x = pos[0] - lengths_[0]/2.;
               h_pos.data[idx].y = pos[1] - lengths_[1]/2.;
               h_pos.data[idx].z = pos[2] - lengths_[2]/2.;
 
               int type = atomIter->typeId();
               h_vel.data[idx].w = simulation().atomType(type).mass();
               h_pos.data[idx].w = __int_as_scalar(type);
               h_tag.data[idx] = idx;
               h_rtag.data[idx] = idx; 
            }
         }
      }
 
      // Generate random velocities
      generateRandomVelocities(h_vel);
      }


      // Notify that the particle order has changed
      particleDataSPtr_->notifyParticleSort();

      // Initialize integrator (calculate forces and potential energy for step 0)
      integratorSPtr_->prepRun(0);

      // Calculate oldEnergy
      thermoSPtr_->compute(0);
      oldEnergy = thermoSPtr_->getLogValue("kinetic_energy",0);
      oldEnergy += thermoSPtr_->getLogValue("potential_energy",0);

      // Integrate nStep_ steps forward
      for (int iStep = 0; iStep < nStep_; ++iStep) {
         integratorSPtr_->update(iStep);

         // do we need to sort the particles?
         // do not sort at time step 0 to speed up short runs
         if (! (iStep % sorterPeriod_) && iStep)
           sorterSPtr_->update(iStep);
      }


      // Calculate new energy
      thermoSPtr_->compute(nStep_);
      newEnergy = thermoSPtr_->getLogValue("kinetic_energy",nStep_);
      newEnergy += thermoSPtr_->getLogValue("potential_energy",nStep_);

      // Decide whether to accept or reject
      bool accept = random().metropolis( boltzmann(newEnergy-oldEnergy) );

      if (accept) {
         // read back integrated positions 
         ArrayHandle<Scalar4> h_pos(particleDataSPtr_->getPositions(), access_location::host, access_mode::read);
         ArrayHandle<Scalar4> h_vel(particleDataSPtr_->getVelocities(), access_location::host, access_mode::read);
         ArrayHandle<unsigned int> h_tag(particleDataSPtr_->getTags(), access_location::host, access_mode::read);
         ArrayHandle<unsigned int> h_rtag(particleDataSPtr_->getRTags(), access_location::host, access_mode::read);
         for (int iSpec = 0; iSpec < nSpec; ++iSpec) {
            system().begin(iSpec, molIter);
            for ( ; molIter.notEnd(); ++molIter) {
               for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
                  unsigned int idx = h_rtag.data[atomIter->id()]; 
                  atomIter->position() = Vector(h_pos.data[idx].x+lengths_[0]/2.,
                                                h_pos.data[idx].y+lengths_[1]/2.,
                                                h_pos.data[idx].z+lengths_[2]/2.);
               }
            }
         }

         system().pairPotential().buildCellList();
         incrementNAccept();
      } else {
         // not accepted, do nothing
      }

      return accept;
   }
   /*
   * Perform replica exchange move.
   */
   bool ReplicaMove::move()
   {
      MPI::Request request[8];
      MPI::Status  status;
      double myWeight, ptWeight, exponential;
      int    isLeft, iAccept, myPort, ptPort;
      System::MoleculeIterator molIter;
      Molecule::AtomIterator   atomIter;
      int iA;
      
      // Default value for no replica exchange
      isLeft  = -1;
      iAccept = 0;

      if ((myId_ < nProcs_ - 1) && (stepCount_ >= myId_) &&
         ((stepCount_ - myId_) % (nProcs_ - 1)  ==0)) {
         // we are exchanging with processor myId_ + 1
         isLeft = 1;
         ptId_ = myId_ + 1;

      } else if ((myId_ > 0) && (stepCount_ >= myId_ - 1) &&
                ((stepCount_  - (myId_ - 1)) % (nProcs_ -1 ) == 0)) {
         // we are exchanging with processor myId_ - 1
         isLeft = 0;
         ptId_ = myId_ - 1; 
      } 
      if (isLeft == 0 || isLeft == 1) {
         // Set the port value for message tag
         myPort = myId_%2;
         ptPort = ptId_%2;
 
         // Update accumulator
         repxAttempt_[isLeft] += 1;

         // Exchange coupling parameters with partner
         for (int i = 0; i < nParameters_; ++i) {
            request[0] = communicatorPtr_->Irecv(&ptParam_[i], 1, MPI::DOUBLE, ptId_,
                                              TagParam[ptPort]);
            request[1] = communicatorPtr_->Isend(&myParam_[i], 1, MPI::DOUBLE, ptId_,
                                              TagParam[myPort]);
         
            // Synchronizing
            request[0].Wait();
            request[1].Wait();
         }   
         myWeight = system().perturbation().difference(ptParam_);
         
         // Collect tempering weights and make decision
         if (isLeft == 1) {

            // Receive energy difference from the right box
            request[2] = communicatorPtr_->Irecv(&ptWeight, 1, MPI::DOUBLE,
                                                ptId_, TagDecision[ptPort]);
            request[2].Wait();

            exponential = exp(-myWeight - ptWeight);

         } else {

            // Send energy difference to the left box
            request[2] = communicatorPtr_->Isend(&myWeight, 1, MPI::DOUBLE,
                                                 ptId_, TagDecision[myPort]);
            request[2].Wait();
         }

         // Collect tempering weights and make decision
         if (isLeft == 1) {
   
            // Metropolis test
            iAccept = system().simulation().random().
                      metropolis(exponential) ? 1 : 0;

            // Send decision to the right box
            request[3] = communicatorPtr_->Isend(&iAccept, 1, MPI::INT,
                                                 ptId_, TagDecision[myPort]);
            request[3].Wait();

         } else {

            // Receive decision from the left box
            request[3] = communicatorPtr_->Irecv(&iAccept, 1, MPI::INT,
                                                 ptId_, TagDecision[ptPort]);
            request[3].Wait();

         }
         // Exchange particle configurations if the move is accepted
         if (iAccept == 1) {
         
            // Update accumulator
            repxAccept_[isLeft] += 1;

            Vector myBoundary;
            myBoundary = system().boundary().lengths();
                  
            Vector ptBoundary;
                  
            // Accomodate new boundary dimensions.
            request[4] = communicatorPtr_->Irecv(&ptBoundary, 1,
                                                 MpiTraits<Vector>::type, ptId_, TagConfig[ptPort]);

            // Send old boundary dimensions.
            request[5] = communicatorPtr_->Isend(&myBoundary, 1,
                                                  MpiTraits<Vector>::type, ptId_, TagConfig[myPort]);

            request[4].Wait();
            request[5].Wait();
                   
            system().boundary().setOrthorhombic(ptBoundary);

            // Pack atomic positions and types.
            iA = 0;
            for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
               for (system().begin(iSpec, molIter); molIter.notEnd(); ++molIter){
                  for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
                     myPositionPtr_[iA] = atomIter->position();
                     iA++;
                  }
               }
            }
            
            // Accomodate new configuration.
            request[6] = communicatorPtr_->Irecv(ptPositionPtr_, iA,
                             MpiTraits<Vector>::type, ptId_, TagConfig[ptPort]);

            // Send old configuration.
            request[7] = communicatorPtr_->Isend(myPositionPtr_, iA,
                             MpiTraits<Vector>::type, ptId_, TagConfig[myPort]);

            request[6].Wait();
            request[7].Wait();
            
            // Adopt the new atomic positions.
            iA = 0;
            for (int iSpec=0; iSpec < system().simulation().nSpecies(); ++iSpec){
               for (system().begin(iSpec, molIter); molIter.notEnd(); ++molIter){
                  for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter){
                     atomIter->position() = ptPositionPtr_[iA];
                     ++iA;
                  }
               }
            }
            

            // Notify component observers.
            //notifyObservers(ptId_);
            Notifier<int>::notifyObservers(ptId_);

         }  else {
            // the move was not accepted, do nothing
         }

      }


      // Output results needed to build exchange profile.
      if (isLeft == -1) {
        outputFile_ << "n" << std::endl;
      } else if ( isLeft != -1 && iAccept == 0) {
        outputFile_ << myId_ << std::endl;
      } else if ( isLeft != -1 && iAccept == 1) {
        outputFile_ << ptId_ << std::endl;
      }

      stepCount_++;

      return (iAccept == 1 ? true : false);

   }