예제 #1
0
   bool ClusterIdentifier::isValid() const
   {
      // Check clusters
      int nCluster = clusters_.size();
      int nMolecule = 0;
      for (int i = 0; i < nCluster; ++i) {
         if (!clusters_[i].isValid()) {
            UTIL_THROW("Invalid cluster");
         }
         nMolecule += clusters_[i].size();
      }
      if (nMolecule != systemPtr_->nMolecule(speciesId_)) {
         UTIL_THROW("Error in number of molecules");
      }
   
      // Check molecules and links
      ClusterLink const * linkPtr;
      System::ConstMoleculeIterator molIter;
      systemPtr_->begin(speciesId_, molIter);
      for ( ; molIter.notEnd(); ++molIter) {

         linkPtr = &(links_[molIter->id()]);
         if (&(linkPtr->molecule()) != molIter.get()) {
            UTIL_THROW("Link without correct molecule association");
         }
         if (linkPtr->clusterId() == -1) {
            UTIL_THROW("Unmarked molecule");
         }
      }

      // Normal return (no errors)
      return true;
   }
예제 #2
0
   void CompositionProfile::sample(long iStep) 
   {
      Vector blengths;

      // Lengths of simulation box
      blengths = system().boundary().lengths();

      if (isAtInterval(iStep))  {

         Vector  position;
         double  product;
         System::ConstMoleculeIterator  molIter;
         Molecule::ConstAtomIterator  atomIter;
         int  nSpecies, iSpecies, typeId;

         // Loop over all atoms
         nSpecies = system().simulation().nSpecies();
         for (iSpecies = 0; iSpecies < nSpecies; ++iSpecies) {
            system().begin(iSpecies, molIter); 
          
            for ( ; molIter.notEnd(); ++molIter) {
               molIter->begin(atomIter); 
          
               for ( ; atomIter.notEnd(); ++atomIter) {
                  position = atomIter->position();
                  typeId   = atomIter->typeId();
                  for (int i = 0; i < Dimension; ++i) {
                     position[i] /= blengths[i];
                  }
		  // Loop over direction vectors
                  for (int i = 0; i < nDirection_; ++i) {
                     product = position.dot(waveVectors_[i]);
                     product /= waveVectors_[i].abs();
                     accumulators_[i+typeId*nDirection_].sample(product);
                  }
		 
               }
  
            }
         }

      ++nSample_;

      }

   }
   void CompositionProfile::sample(long iStep) 
   {
      Vector blengths;

      // Lengths of simulation box
      blengths = system().boundary().lengths();

      if (isAtInterval(iStep))  {
         Vector  position;
         double  product;
         System::ConstMoleculeIterator  molIter;
         Molecule::ConstAtomIterator  atomIter;
         int  nSpecies, iSpecies, typeId;

         // Clear accumulators for the current timestep
         for (int i = 0; i < nDirection_; ++i) {
            for (int j = 0; j < nAtomType_; ++j){
               currentAccumulators_[i+j*nDirection_].clear();
            }
         } 

         // Select open mode for output files
         std::ios_base::openmode mode = std::ios_base::out;
         if (!isFirstStep_) {
           mode = std::ios_base::out | std::ios_base::app; 
         }

         // Open log files
         for (int i = 0; i < nDirection_; ++i) {
            for (int j = 0; j < nAtomType_; ++j){
                std::ostringstream oss;
                oss << outputFileName();
                
                for (int k = 0; k < Dimension; ++k) {
                    oss << "_" << intVectors_[i][k];
                }
                oss << "_type" << j << ".log";

                fileMaster().openOutputFile(oss.str(), 
                                            logFiles_[i+j*nDirection_], 
                                            mode);
            }
         }

         // Loop over all atoms
         nSpecies = system().simulation().nSpecies();
         for (iSpecies = 0; iSpecies < nSpecies; ++iSpecies) {
            system().begin(iSpecies, molIter); 
          
            for ( ; molIter.notEnd(); ++molIter) {
               molIter->begin(atomIter); 
          
               for ( ; atomIter.notEnd(); ++atomIter) {
                  position = atomIter->position();
                  typeId   = atomIter->typeId();
                  for (int i = 0; i < Dimension; ++i) {
                     position[i] /= blengths[i];
                  }
	              // Loop over direction vectors
                  for (int i = 0; i < nDirection_; ++i) {
                     product = position.dot(waveVectors_[i]);
                     product /= waveVectors_[i].abs();
                     accumulators_[i+typeId*nDirection_].sample(product);
                     currentAccumulators_[i+typeId*nDirection_].sample(product);
                  }
		 
               }
  
            }
         }

      ++nSample_;

      // Output to log files
      for (int i = 0; i < nDirection_; ++i) {
         for (int j = 0; j < nAtomType_; ++j){
            currentAccumulators_[i+j*nDirection_].output(logFiles_[i+j*nDirection_]);
            logFiles_[i+j*nDirection_] << std::endl;
         }
      }

      // Close log files
      for (int i = 0; i < nDirection_; ++i) {
         for (int j = 0; j < nAtomType_; ++j){
            logFiles_[i+j*nDirection_].close();
         }
      }

      isFirstStep_ = false;
      }

   }
예제 #4
0
/*
* Increment Structure Factor
*/
void IntraStructureFactor::sample(long iStep)
{
    if (isAtInterval(iStep))  {

        Vector  position;
        std::complex<double> rho[2];
        std::complex<double> expFactor;
        double  volume = system().boundary().volume();
        double  product, dS;
        System::ConstMoleculeIterator molIter;
        Molecule::ConstAtomIterator   atomIter;
        int  typeId, i, j, k;

        makeWaveVectors();

        // Set all Deltas to zero
        for (i = 0; i < nWave_; ++i) {
            for (int pairId = 0; pairId < nAtomTypeIdPair_; ++pairId) {
                structureFactorDelta_(i, pairId) = 0;
            }
        }

        // Loop over molecules in species
        system().begin(speciesId_, molIter);
        for ( ; molIter.notEnd(); ++molIter) {

            // Set all Fourier modes to zero
            for (i = 0; i < nWave_; ++i) {
                for (typeId = 0; typeId <= nAtomType_; ++typeId) {
                    fourierModes_(i, typeId) = 0;
                }
            }

            // Loop over all atoms in one molecule
            molIter->begin(atomIter);
            for ( ; atomIter.notEnd(); ++atomIter) {
                position = atomIter->position();
                typeId   = atomIter->typeId();

                // Loop over wavevectors
                for (i = 0; i < nWave_; ++i) {
                    product = position.dot(waveVectors_[i]);
                    expFactor = exp( product*Constants::Im );
                    fourierModes_(i, typeId)     += expFactor;
                    fourierModes_(i, nAtomType_) += expFactor;
                }

            }

            // Increment structure factors
            for (i = 0; i < nWave_; ++i) {
                for (j = 0; j < nAtomTypeIdPair_; ++j) {
                    for (k = 0; k < 2; ++k) {
                        typeId = atomTypeIdPairs_[j][k];
                        if (typeId >= 0) {
                            rho[k] = fourierModes_(i, typeId);
                        } else {
                            rho[k] = fourierModes_(i, nAtomType_);
                        }
                    }
                    rho[0] = std::conj(rho[0]);
                    dS = std::real(rho[0]*rho[1])/volume;
                    structureFactors_(i, j) += dS;
                    structureFactorDelta_(i,j) += dS;
                }
            }

        }

        ++nSample_;
    }

}
예제 #5
0
   /* 
   * Increment structure factors for all wavevectors and modes.
   */
   void StructureFactor::sample(long iStep) 
   {
      if (isAtInterval(iStep))  {

         fileMaster().openOutputFile(outputFileName("_max.dat"), outputFile_, !isFirstStep_);
         isFirstStep_ = false;

         Vector  position;
         std::complex<double>  expFactor;
         double  product;
         System::ConstMoleculeIterator  molIter;
         Molecule::ConstAtomIterator  atomIter;
         int  nSpecies, iSpecies, typeId, i, j;

         makeWaveVectors();

         // Set all Fourier modes to zero
         for (i = 0; i < nWave_; ++i) {
            for (j = 0; j < nMode_; ++j) {
               fourierModes_(i, j) = std::complex<double>(0.0, 0.0);
            }
         }
 
         // Loop over all atoms
         nSpecies = system().simulation().nSpecies();
         for (iSpecies = 0; iSpecies < nSpecies; ++iSpecies) {
            system().begin(iSpecies, molIter); 
            for ( ; molIter.notEnd(); ++molIter) {
               molIter->begin(atomIter); 
               for ( ; atomIter.notEnd(); ++atomIter) {
                  position = atomIter->position();
                  typeId   = atomIter->typeId();
 
		  // Loop over wavevectors
                  for (i = 0; i < nWave_; ++i) {
               
                     product = position.dot(waveVectors_[i]);
                     expFactor = exp( product*Constants::Im );
                     for (j = 0; j < nMode_; ++j) {
                        fourierModes_(i, j) += modes_(j, typeId)*expFactor;
                     }
		 
                  }
  
               }
            }

         }

         // Increment structure factors
         double volume = system().boundary().volume();
         double norm;
         for (j = 0; j < nMode_; ++j) {
            double maxValue = 0.0;
            IntVector maxIntVector;
            double maxQ;
            for (i = 0; i < nWave_; ++i) {
               norm = std::norm(fourierModes_(i, j));
               if (double(norm/volume) >= maxValue) {
                  maxValue = double(norm/volume);
                  maxIntVector = waveIntVectors_[i];
                  maxQ = waveVectors_[i].abs();
               }
               structureFactors_(i, j) += norm/volume;
            }

            // Output current maximum S(q)
            outputFile_ << maxIntVector;
            outputFile_ << Dbl(maxQ,20,8);
            outputFile_ << Dbl(maxValue,20,8);
            outputFile_ << std::endl;
         }

         ++nSample_;

         outputFile_ << std::endl;
         outputFile_.close();
      }

   }
예제 #6
0
   /// Increment Structure Factor
   void GPUStructureFactorGrid::sample(long iStep)
   {
      if (isAtInterval(iStep))  {
  
         Vector  position;
         System::ConstMoleculeIterator  molIter;
         Molecule::ConstAtomIterator  atomIter;
         int  nSpecies, iSpecies, typeId, i, j;

         makeWaveVectors();

        
         // allocate temporary arrays
         int nType = system().simulation().nAtomType();

         float3 *h_wave_vectors = new float3[nWave_];
         float3 *h_pos = new float3[system().simulation().atomCapacity()];
         int *h_type = new int[system().simulation().atomCapacity()];
         float *h_mode = new float[nMode_*nType];
         float *h_sq = new float[nMode_*nWave_];

         // Load wave vectors
         for (int i = 0; i < nWave_; i++)
            h_wave_vectors[i] = make_float3((float) waveVectors_[i][0],
                                             (float) waveVectors_[i][1],
                                             (float) waveVectors_[i][2]);

         // Load atoms into temporary storage
         nSpecies = system().simulation().nSpecies();
         int nAtom = 0;
         for (iSpecies = 0; iSpecies < nSpecies; ++iSpecies) {
            system().begin(iSpecies, molIter);
            for ( ; molIter.notEnd(); ++molIter) {
               molIter->begin(atomIter);
               for ( ; atomIter.notEnd(); ++atomIter) {
                  position = atomIter->position();
                  typeId   = atomIter->typeId();

                  h_pos[nAtom] = make_float3(position[0],position[1],position[2]);
                  h_type[nAtom] = typeId;
                  nAtom++;
                  }

               }
            }

         // Load modes
         for (i = 0; i < nMode_; ++i) {
            for (j = 0; j < nType; ++j) {
               h_mode[nType*i + j] = modes_(i, j);
            }
         }
            
         // Calculate structure factors
         int res = gpu_sample_structure_factor(nWave_,
                                     h_wave_vectors,
                                     nAtom,
                                     h_pos,
                                     h_type,
                                     nType,
                                     nMode_,
                                     h_mode,
                                     h_sq,
                                     system().boundary().volume()
                                     );
          
         if (res)
             UTIL_THROW("Error updating structure factor.");

         // increment structure factors
         for (j = 0; j < nMode_; ++j) {
            double maxValue = 0.0;
            IntVector maxIntVector;
            double maxQ;
            for (i = 0; i < nWave_; ++i) {
               if ((double) h_sq[j*nWave_+i] >= maxValue) {
                  maxValue = (double) h_sq[j*nWave_+i];
                  maxIntVector = waveIntVectors_[i];
                  maxQ = waveVectors_[i].abs();
               }
               structureFactors_(i, j) += (double) h_sq[j*nWave_ + i];
            }
          //maximumValue_[j].insert(maximumValue_[j].end(), 1, maxValue);
          //maximumWaveIntVector_[j].insert(maximumWaveIntVector_[j].end(), 1, maxIntVector);
          //maximumQ_[j].insert(maximumQ_[j].end(), 1, maxQ);
         }

         delete [] h_wave_vectors;
         delete [] h_pos;
         delete [] h_mode;
         delete [] h_type;
         delete [] h_sq;

          ++nSample_;

      }
   }    
예제 #7
0
   /* 
   * Write the configuration file.
   */
   void McMdConfigIo::write(std::ostream &out)
   {
      using std::endl;

      // Write Boundary dimensions
      out << "BOUNDARY" << endl << endl;
      out << boundary() << endl;

      // Write atomic positions
      System::ConstMoleculeIterator molIter;
      Molecule::ConstAtomIterator   atomIter;
      Species* speciesPtr;
      int iSpecies, iMolecule;
      out << endl << "MOLECULES" << endl;
      for (iSpecies = 0; iSpecies < simulation().nSpecies(); ++iSpecies) {
         out << endl;
         out << "species    " << iSpecies << endl;
         out << "nMolecule  " << system().nMolecule(iSpecies) << endl;
         speciesPtr = &simulation().species(iSpecies);
         iMolecule = 0;
         system().begin(iSpecies, molIter); 
         for ( ; molIter.notEnd(); ++molIter) {
            out << endl;
            out << "molecule   " << iMolecule << endl;
            if (speciesPtr->isMutable()) {
               speciesPtr->mutator().writeMoleculeState(out, *molIter);
            }
            for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
               //out << atomIter->position() << endl;
               writeAtom(out, *atomIter);
            }
            ++iMolecule;
         }
      }

      #ifdef INTER_TETHER
      { // Scope for local variables

         // Write Tethers
         Tether*   tetherPtr;
         Atom*     atomPtr;
         Molecule* molPtr;
         int       iTether, nTether, iAtom;
         out << std::endl;
         out << "TETHERS" << endl << endl;
         nTether = system().tetherMaster().nTether();
         out << Label("nTether") << nTether << std::endl;
         for (iTether = 0; iTether < nTether; ++iTether) {
            tetherPtr = &(system().tetherMaster().tether(iTether));
            atomPtr   = &tetherPtr->atom();
            molPtr    = &atomPtr->molecule();
            iAtom     = atomPtr->indexInMolecule();
            iMolecule = system().moleculeId(*molPtr);
            iSpecies  = molPtr->species().id();
            out << Int(iSpecies,5) << Int(iMolecule,9) << Int(iAtom,6) 
                << tetherPtr->anchor() << std::endl;
         }

      }
      #endif

      #ifdef MCMD_LINK
      { // Scope for local variables

         // Write Links
         Link*      linkPtr;
         Atom*      atomPtr;
         Molecule*  molPtr;
         int        iLink, nLink, iAtom;
         out << std::endl;
         out << "LINKS" << endl << endl;
         nLink = system().linkMaster().nLink();
         out << Label("nLink") << nLink << std::endl;
         for (iLink = 0; iLink < nLink; ++iLink) {
            linkPtr  = &(system().linkMaster().link(iLink));

            // Output species, molecule, atom ids for atom 0
            atomPtr   = &(linkPtr->atom0());
            molPtr    = &atomPtr->molecule();
            iAtom     = atomPtr->indexInMolecule();
            iMolecule = system().moleculeId(*molPtr);
            iSpecies  = molPtr->species().id();
            out << Int(iSpecies,8) << Int(iMolecule,8) << Int(iAtom,8);
            out << "   ";

            // Output species, molecule, atom ids for atom 1
            atomPtr   = &(linkPtr->atom1());
            molPtr    = &atomPtr->molecule();
            iAtom     = atomPtr->indexInMolecule();
            iMolecule = system().moleculeId(*molPtr);
            iSpecies  = molPtr->species().id();
            out << Int(iSpecies,8) << Int(iMolecule,8) << Int(iAtom,8);
            out << "   ";

            out << Int(linkPtr->typeId(),8) << std::endl;
         }

      }
      #endif

   }