/*
* Initialize all Angle objects for Molecules of one Species.
*
* This functions assigns pointers to Atoms and angle types ids within a
* contiguous block of Angle objects, and sets a pointer in each Molecule
* to the first Angle in the associated block.
*/
void Simulation::initializeSpeciesAngles(int iSpecies)
{
if (nAngleType_ <= 0) {
UTIL_THROW("nAngleType must be positive");
}
Species* speciesPtr = 0;
Molecule *moleculePtr = 0;
Angle *anglePtr = 0;
Atom *firstAtomPtr, *atom0Ptr, *atom1Ptr, *atom2Ptr;
int iMol, iAngle, atom0Id, atom1Id, atom2Id, type;
int capacity, nAngle;
speciesPtr = &species(iSpecies);
capacity = speciesPtr->capacity();
nAngle = speciesPtr->nAngle();
// Initialize pointers before loop
moleculePtr = &molecules_[firstMoleculeIds_[iSpecies]];
anglePtr = &angles_[firstAngleIds_[iSpecies]];
// Loop over molecules in Species
for (iMol = 0; iMol < capacity; ++iMol) {
firstAtomPtr = &(moleculePtr->atom(0));
moleculePtr->setFirstAngle(*anglePtr);
moleculePtr->setNAngle(nAngle);
if (nAngle > 0) {
// Create angles for a molecule
for (iAngle = 0; iAngle < nAngle; ++iAngle) {
// Get pointers to atoms spanning the angle and angle type
atom0Id = speciesPtr->speciesAngle(iAngle).atomId(0);
atom1Id = speciesPtr->speciesAngle(iAngle).atomId(1);
atom2Id = speciesPtr->speciesAngle(iAngle).atomId(2);
type = speciesPtr->speciesAngle(iAngle).typeId();
atom0Ptr = firstAtomPtr + atom0Id;
atom1Ptr = firstAtomPtr + atom1Id;
atom2Ptr = firstAtomPtr + atom2Id;
// Set fields of the Angle object
anglePtr->setAtom(0, *atom0Ptr);
anglePtr->setAtom(1, *atom1Ptr);
anglePtr->setAtom(2, *atom2Ptr);
anglePtr->setTypeId(type);
++anglePtr;
}
}
++moleculePtr;
}
}
