/*
* 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;
}
}
/*
* 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
// Increment total capacity values
capacity = speciesPtr->capacity();
nAtom = speciesPtr->nAtom();
moleculeCapacity_ += capacity;
atomCapacity_ += capacity*nAtom;
if (nBondType_ > 0) {
nBond = speciesPtr->nBond();
bondCapacity_ += capacity*nBond;
}
#ifdef INTER_ANGLE
if (nAngleType_ > 0) {
nAngle = speciesPtr->nAngle();
angleCapacity_ += capacity*nAngle;
}
#endif
#ifdef INTER_DIHEDRAL
if (nDihedralType_ > 0) {
nDihedral = speciesPtr->nDihedral();
dihedralCapacity_ += capacity*nDihedral;
}
#endif
}
// Allocate global array of atoms (static member of Atom class).
Atom::allocate(atomCapacity_, atoms_);
// Allocate other global arrays (members of Simulation).
molecules_.allocate(moleculeCapacity_);
// Initialize all Atoms and Molecule objects.
for (iSpecies = 0; iSpecies < nSpecies(); ++iSpecies) {
speciesPtr = &species(iSpecies);
initializeSpecies(iSpecies);
}
// Initialize bonds.
if (nBondType_ > 0) {
if (bondCapacity_ > 0) {
bonds_.allocate(bondCapacity_);
} else {
bonds_.allocate(1);
}
for (iSpecies = 0; iSpecies < nSpecies(); ++iSpecies) {
initializeSpeciesBonds(iSpecies);
}
}
#ifdef INTER_ANGLE
// Initialize angles.
if (nAngleType_ > 0) {
if (angleCapacity_ > 0) {
angles_.allocate(angleCapacity_);
} else {
angles_.allocate(1);
}
for (iSpecies = 0; iSpecies < nSpecies(); ++iSpecies) {
initializeSpeciesAngles(iSpecies);
}
}
#endif
#ifdef INTER_DIHEDRAL
// Initialize dihedrals.
if (nDihedralType_ > 0) {
if (dihedralCapacity_ > 0) {
dihedrals_.allocate(dihedralCapacity_);
} else {
dihedrals_.allocate(1);
}
for (iSpecies = 0; iSpecies < nSpecies(); ++iSpecies) {
initializeSpeciesDihedrals(iSpecies);
}
}
#endif
}