/*
* Read input parameters.
*/
void MdPairEnergyCoefficients::readParameters(std::istream& in)
{
readInterval(in);
readOutputFileName(in);
read<PairSelector>(in, "selector", selector_);
read<int>(in, "maxMoleculeNeighbors", maxMoleculeNeighbors_);
// Allocate
int iSpecies;
moleculeNeighbors_.allocate(nSpecies_);
twoMoleculePairEnergy_.allocate(nSpecies_);
for (iSpecies = 0; iSpecies < nSpecies_; ++iSpecies) {
Species *speciesPtr;
int nMolecule;
int iMolecule;
speciesPtr = &system().simulation().species(iSpecies);
nMolecule = speciesPtr->capacity();
moleculeNeighbors_[iSpecies].allocate(nMolecule);
twoMoleculePairEnergy_[iSpecies].allocate(nMolecule);
for (iMolecule = 0; iMolecule < nMolecule; ++iMolecule) {
moleculeNeighbors_[iSpecies][iMolecule].
allocate(maxMoleculeNeighbors_);
}
}
fileMaster().openOutputFile(outputFileName(".dat"), outputFile_);
isInitialized_ = true;
}
/*
* 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 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;
}
}
/*
* Initialize all Dihedral objects for Molecules of one Species.
*
* This functions assigns pointers to Atoms and Dihedral types ids within
* a contiguous block of Dihedral objects, and sets a pointer in each
* Molecule to the first Dihedral in the associated block.
*/
void Simulation::initializeSpeciesDihedrals(int iSpecies)
{
Species* speciesPtr = 0;
Molecule *moleculePtr = 0;
Dihedral *dihedralPtr = 0;
Atom *firstAtomPtr, *atom0Ptr, *atom1Ptr, *atom2Ptr, *atom3Ptr;
int iMol, iDihedral, atom0Id, atom1Id, atom2Id, atom3Id, type;
int capacity, nDihedral;
speciesPtr = &species(iSpecies);
capacity = speciesPtr->capacity();
nDihedral = speciesPtr->nDihedral();
// Initialize pointers before loop
moleculePtr = &molecules_[firstMoleculeIds_[iSpecies]];
dihedralPtr = &dihedrals_[firstDihedralIds_[iSpecies]];
// Loop over molecules in Species
for (iMol = 0; iMol < capacity; ++iMol) {
firstAtomPtr = &(moleculePtr->atom(0));
moleculePtr->setFirstDihedral(*dihedralPtr);
moleculePtr->setNDihedral(nDihedral);
if (nDihedral > 0) {
// Create dihedrals for a molecule
for (iDihedral = 0; iDihedral < nDihedral; ++iDihedral) {
// Get local indices for atoms and dihedral type
atom0Id = speciesPtr->speciesDihedral(iDihedral).atomId(0);
atom1Id = speciesPtr->speciesDihedral(iDihedral).atomId(1);
atom2Id = speciesPtr->speciesDihedral(iDihedral).atomId(2);
atom3Id = speciesPtr->speciesDihedral(iDihedral).atomId(3);
type = speciesPtr->speciesDihedral(iDihedral).typeId();
// Calculate atom pointers
atom0Ptr = firstAtomPtr + atom0Id;
atom1Ptr = firstAtomPtr + atom1Id;
atom2Ptr = firstAtomPtr + atom2Id;
atom3Ptr = firstAtomPtr + atom3Id;
// Set fields of the Dihedral object
dihedralPtr->setAtom(0, *atom0Ptr);
dihedralPtr->setAtom(1, *atom1Ptr);
dihedralPtr->setAtom(2, *atom2Ptr);
dihedralPtr->setAtom(3, *atom3Ptr);
dihedralPtr->setTypeId(type);
++dihedralPtr;
}
}
++moleculePtr;
}
}
/*
* Load state from an archive.
*/
void MdPairEnergyCoefficients::loadParameters(Serializable::IArchive& ar)
{
loadInterval(ar);
loadOutputFileName(ar);
fileMaster().openOutputFile(outputFileName(".dat"), outputFile_);
loadParameter<PairSelector>(ar, "selector", selector_);
loadParameter<int>(ar, "maxMoleculeNeighbors", maxMoleculeNeighbors_);
int nAtomType, nSpecies;
ar & nAtomType;
ar & nSpecies;
if (nAtomType != nAtomType_) {
UTIL_THROW("Inconsistent values of nAtomType");
}
if (nSpecies != nSpecies_) {
UTIL_THROW("Inconsistent values of nSpecies");
}
// Allocate moleculeNeighbors and twoMoleculePairEnergy.
int iSpecies;
moleculeNeighbors_.allocate(nSpecies_);
twoMoleculePairEnergy_.allocate(nSpecies_);
for (iSpecies = 0; iSpecies < nSpecies_; ++iSpecies) {
Species *speciesPtr;
int nMolecule;
int iMolecule;
speciesPtr = &system().simulation().species(iSpecies);
nMolecule = speciesPtr->capacity();
moleculeNeighbors_[iSpecies].allocate(nMolecule);
twoMoleculePairEnergy_[iSpecies].allocate(nMolecule);
for (iMolecule = 0; iMolecule < nMolecule; ++iMolecule) {
moleculeNeighbors_[iSpecies][iMolecule].
allocate(maxMoleculeNeighbors_);
}
}
ar & pairEnergyAccumulator_;
ar & moleculePESqAccumulator_;
ar & twoMoleculePESqAccumulator_;
ar & pESqAccumulator_;
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;
}
}
/*
* Initial setup.
*/
void
ClusterIdentifier::initialize(int speciesId, int atomTypeId, double cutoff)
{
// Set member variables
speciesId_ = speciesId;
atomTypeId_ = atomTypeId;
cutoff_ = cutoff;
// Allocate memory
Species* speciesPtr = &system().simulation().species(speciesId);
int moleculeCapacity = speciesPtr->capacity();
links_.allocate(moleculeCapacity);
clusters_.reserve(64);
int atomCapacity = system().simulation().atomCapacity();
cellList_.setAtomCapacity(atomCapacity);
// Note: We must set the cellist atom capacity to the total atom capacity,
// even though we are only interested in clusters of one species, because
// the celllist atom capacity sets the maximum allowed atom index value.
}
/*
* 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;
}
}
/*
* 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
}
