C++ Species::nBond方法代码示例

   /*
   * Initialize all Bond objects for Molecules of one Species. (private)
   *
   * This functions assigns pointers to Atoms and bond types ids within a
   * contiguous block of Bond objects, and sets a pointer in each Molecule
   * to the first Bond in the associated block.
   */
   void Simulation::initializeSpeciesBonds(int iSpecies)
   {
      if (nBondType_ <= 0) {
         UTIL_THROW("nBondType_ must be positive");
      }

      Species*  speciesPtr = 0;
      Molecule* moleculePtr = 0;
      Bond*     bondPtr = 0;
      Atom*     firstAtomPtr;
      Atom*     atom0Ptr;
      Atom*     atom1Ptr;
      int       iMol, iBond, atom0Id, atom1Id, type;
      int       capacity, nBond;

      speciesPtr = &species(iSpecies);
      nBond      = speciesPtr->nBond();
      capacity   = speciesPtr->capacity();

      // Initialize pointers before loop
      moleculePtr = &molecules_[firstMoleculeIds_[iSpecies]];
      bondPtr = &bonds_[firstBondIds_[iSpecies]];

      // Loop over molecules in Species
      for (iMol = 0; iMol < capacity; ++iMol) {

         firstAtomPtr = &(moleculePtr->atom(0));
         moleculePtr->setFirstBond(*bondPtr);
         moleculePtr->setNBond(nBond);

         if (nBond > 0) {

            // Create bonds for a molecule
            for (iBond = 0; iBond < nBond; ++iBond) {

               // Get pointers to bonded atoms and bond type
               atom0Id  = speciesPtr->speciesBond(iBond).atomId(0);
               atom1Id  = speciesPtr->speciesBond(iBond).atomId(1);
               type     = speciesPtr->speciesBond(iBond).typeId();
               atom0Ptr = firstAtomPtr + atom0Id;
               atom1Ptr = firstAtomPtr + atom1Id;

               // Set fields of the Bond object
               bondPtr->setAtom(0, *atom0Ptr);
               bondPtr->setAtom(1, *atom1Ptr);
               bondPtr->setTypeId(type);

               // If MaskBonded, add each bonded atom to its partners Mask
               if (maskedPairPolicy_ == MaskBonded) {
                  atom0Ptr->mask().append(*atom1Ptr);
                  atom1Ptr->mask().append(*atom0Ptr);
               }

               ++bondPtr;
            }

         }
         ++moleculePtr;
      }

   }

   /*
   * Allocate and initialize all private data (private method).
   *
   * Allocates global arrays (molecules_, atoms_, bonds_, angles_) and the
   * arrays first<class>Ids_ of integers to species blocks. Initializes:
   *
   *   - Capacity values and first<class>Ptr_ addresses.
   *   - Integer ids for Species and Molecule objects.
   *   - Pointers between Species, Molecule, and Atom objects
   *   - Atom typeIds and all Bond and Angle objects.
   */
   void Simulation::initialize()
   {
      //Preconditions
      assert(nSpecies() > 0);
      if (nSpecies() <= 0) {
         UTIL_THROW("Error: nSpecies() <= 0 in Simulation::initialize()");
      }
      if (nBondType_ < 0) {
         UTIL_THROW("Error: nBondType < 0 in Simulation::initialize()");
      }
      #ifdef INTER_ANGLE
      if (nAngleType_ < 0) {
         UTIL_THROW("Error: nAngleType < 0 in Simulation::initialize()");
      }
      #endif
      #ifdef INTER_DIHEDRAL
      if (nDihedralType_ < 0) {
         UTIL_THROW("Error: nDihedralType < 0 in Simulation::initialize()");
      }
      #endif
      #ifdef MCMD_LINK
      if (nLinkType_ < 0) {
         UTIL_THROW("Error: nLinkType_ < 0 in Simulation::initialize()");
      }
      #endif

      Species *speciesPtr;
      int  nAtom, nBond, iSpecies;
      int capacity;
      #ifdef INTER_ANGLE
      int  nAngle;
      #endif
      #ifdef INTER_DIHEDRAL
      int  nDihedral;
      #endif

      // Allocate arrays of pointers to first object in a species block.
      firstMoleculeIds_.allocate(nSpecies());
      firstAtomIds_.allocate(nSpecies());
      if (nBondType_ > 0) {
         firstBondIds_.allocate(nSpecies());
      }
      #ifdef INTER_ANGLE
      if (nAngleType_ > 0) {
         firstAngleIds_.allocate(nSpecies());
      }
      #endif
      #ifdef INTER_DIHEDRAL
      if (nDihedralType_ > 0) {
         firstDihedralIds_.allocate(nSpecies());
      }
      #endif

      // Count Molecules, Atoms and Groups.
      moleculeCapacity_ = 0;
      atomCapacity_     = 0;
      bondCapacity_     = 0;
      #ifdef INTER_ANGLE
      angleCapacity_    = 0;
      #endif
      #ifdef INTER_DIHEDRAL
      dihedralCapacity_  = 0;
      #endif
      for (iSpecies = 0; iSpecies < nSpecies(); ++iSpecies) {
         speciesPtr = &species(iSpecies);

         // Check species id
         if (speciesPtr->id() != iSpecies) {
            UTIL_THROW("Inconsistent species ids");
         }
         //speciesPtr->setId(iSpecies);

         // Set indexes of first objects of the blocks for this species
         firstMoleculeIds_[iSpecies] = moleculeCapacity_;
         firstAtomIds_[iSpecies] = atomCapacity_;
         if (nBondType_ > 0) {
            firstBondIds_[iSpecies] = bondCapacity_;
         }
         #ifdef INTER_ANGLE
         if (nAngleType_ > 0) {
            firstAngleIds_[iSpecies] = angleCapacity_;
         }
         #endif
         #ifdef INTER_DIHEDRAL
         if (nDihedralType_ > 0) {
            firstDihedralIds_[iSpecies] = dihedralCapacity_;
         }
         #endif

//.........这里部分代码省略.........