/*
* 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;
}
}
