/*
* Read parameter speciesId.
*/
void EndSwapMove::readParameters(std::istream& in)
{
readProbability(in);
read<int>(in, "speciesId", speciesId_);
Species* speciesPtr = &(simulation().species(speciesId_));
int nAtom = speciesPtr->nAtom();
// Preconditions
if (speciesPtr->isMutable()) {
UTIL_THROW("EndSwapMove on mutable Species");
}
Linear* linearPtr = dynamic_cast<Linear*>(speciesPtr);
if (linearPtr == 0) {
UTIL_THROW("EndSwapMove on Species that is not a Linear");
}
// Allocate memory
atomTypeIds_.allocate(nAtom);
positions_.allocate(nAtom);
// Set array of atom type ids
for (int i = 0; i < nAtom; ++i) {
atomTypeIds_[i] = speciesPtr->atomTypeId(i);
}
}
/*
* Load state from a binary file archive.
*/
void McMuExchange::loadParameters(Serializable::IArchive& ar)
{
loadInterval(ar);
loadOutputFileName(ar);
loadParameter(ar, "speciesId", speciesId_);
ar >> nAtom_;
Species* speciesPtr;
speciesPtr = &(system().simulation().species(speciesId_));
if (nAtom_ != speciesPtr->nAtom()) {
UTIL_THROW("Inconsistent values of nAtom on loading");
}
newTypeIds_.allocate(nAtom_);
loadDArray(ar, "newTypeIds", newTypeIds_, nAtom_);
flipAtomIds_.allocate(nAtom_);
isAtomFlipped_.allocate(nAtom_);
for (int i = 0; i < nAtom_; ++i) {
if (newTypeIds_[i] != speciesPtr->atomTypeId(i)) {
flipAtomIds_.append(i);
isAtomFlipped_[i] = 1;
} else {
isAtomFlipped_[i] = 0;
}
}
accumulators_.allocate(speciesPtr->capacity());
ar >> nMolecule_;
for (int i = 0; i < nMolecule_; ++i) {
ar >> accumulators_[i];
}
isInitialized_ = true;
}
/*
* Initialize all Molecule and Atom objects for one Species (private).
*
* This function creates associations between Species, Molecule, and
* Atom objects for all molecules of one species, and sets atom typeIds.
*
* For each molecule, it sets the id, species pointer, nAtom, and the
* firstAtom pointer. The molecule id is only unique within each species.
*
* For each atom, it sets the molecule pointer and an integer typeId.
*
* This method also pushes all molecules of the species onto the
* reservoir, pushing them in order of decreasing molecule id.
*/
void Simulation::initializeSpecies(int iSpecies)
{
Species* speciesPtr;
Molecule* moleculePtr;
Atom* atomPtr;
int iMol, iAtom;
int capacity, nAtom;
speciesPtr = &species(iSpecies);
capacity = speciesPtr->capacity();
nAtom = speciesPtr->nAtom();
// Initialize pointers before loop
moleculePtr = &molecules_[firstMoleculeIds_[iSpecies]];
atomPtr = &atoms_[firstAtomIds_[iSpecies]];
// Loop over all molecules in Species
for (iMol = 0; iMol < capacity; ++iMol) {
// Initialize a Molecule
moleculePtr->setId(iMol);
moleculePtr->setSpecies(*speciesPtr);
moleculePtr->setNAtom(nAtom);
moleculePtr->setFirstAtom(*atomPtr);
// Loop over atoms in a molecule, set molecule and atom TypeId
for (iAtom = 0; iAtom < nAtom; ++iAtom) {
atomPtr->setMolecule(*moleculePtr);
atomPtr->setTypeId(speciesPtr->atomTypeId(iAtom));
++atomPtr;
}
++moleculePtr;
}
// Push all molecules of this species onto the reservoir stack
// Push on in reverse order, so that they pop off in sequence
moleculePtr = &molecules_[firstMoleculeIds_[iSpecies] + capacity - 1];
for (iMol = 0; iMol < capacity; ++iMol) {
speciesPtr->reservoir().push(*moleculePtr);
--moleculePtr;
}
}
