/*
* 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;
}
}
/*
* Load from archive.
*/
void EndSwapMove::loadParameters(Serializable::IArchive& ar)
{
McMove::loadParameters(ar);
loadParameter<int>(ar, "speciesId", speciesId_);
ar & atomTypeIds_;
// Validate
Species* speciesPtr = &(simulation().species(speciesId_));
int nAtom = speciesPtr->nAtom();
if (speciesPtr->isMutable()) {
UTIL_THROW("EndSwapMove applied to mutable species");
}
Linear* linearPtr = dynamic_cast<Linear*>(speciesPtr);
if (linearPtr == 0) {
UTIL_THROW("EndSwapMove applied to species that is not Linear");
}
if (nAtom != atomTypeIds_.capacity()) {
UTIL_THROW("Inconsistent capacity for atomTypeIds array");
}
positions_.allocate(nAtom);
}
/*
* 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
}
