C++ Species::nDihedral方法代码示例

   /*
   * Initialize all Dihedral objects for Molecules of one Species.
   *
   * This functions assigns pointers to Atoms and Dihedral types ids within
   * a contiguous block of Dihedral objects, and sets a pointer in each 
   * Molecule to the first Dihedral in the associated block.
   */
   void Simulation::initializeSpeciesDihedrals(int iSpecies)
   {

      Species*  speciesPtr = 0;
      Molecule *moleculePtr = 0;
      Dihedral  *dihedralPtr = 0;
      Atom     *firstAtomPtr, *atom0Ptr, *atom1Ptr, *atom2Ptr, *atom3Ptr;
      int       iMol, iDihedral, atom0Id, atom1Id, atom2Id, atom3Id, type;
      int       capacity, nDihedral;

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

      // Initialize pointers before loop
      moleculePtr = &molecules_[firstMoleculeIds_[iSpecies]];
      dihedralPtr = &dihedrals_[firstDihedralIds_[iSpecies]];

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

         firstAtomPtr = &(moleculePtr->atom(0));
         moleculePtr->setFirstDihedral(*dihedralPtr);
         moleculePtr->setNDihedral(nDihedral);

         if (nDihedral > 0) {

            // Create dihedrals for a molecule
            for (iDihedral = 0; iDihedral < nDihedral; ++iDihedral) {

               // Get local indices for atoms and dihedral type
               atom0Id  = speciesPtr->speciesDihedral(iDihedral).atomId(0);
               atom1Id  = speciesPtr->speciesDihedral(iDihedral).atomId(1);
               atom2Id  = speciesPtr->speciesDihedral(iDihedral).atomId(2);
               atom3Id  = speciesPtr->speciesDihedral(iDihedral).atomId(3);
               type     = speciesPtr->speciesDihedral(iDihedral).typeId();

               // Calculate atom pointers
               atom0Ptr = firstAtomPtr + atom0Id;
               atom1Ptr = firstAtomPtr + atom1Id;
               atom2Ptr = firstAtomPtr + atom2Id;
               atom3Ptr = firstAtomPtr + atom3Id;

               // Set fields of the Dihedral object
               dihedralPtr->setAtom(0, *atom0Ptr);
               dihedralPtr->setAtom(1, *atom1Ptr);
               dihedralPtr->setAtom(2, *atom2Ptr);
               dihedralPtr->setAtom(3, *atom3Ptr);
               dihedralPtr->setTypeId(type);

               ++dihedralPtr;
            }
         }
         ++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

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