/**
* connection to LinkResetEvent
*/
void HoomdMove::update(const LinkResetEvent& event)
{
if (!HoomdIsInitialized_) return;
Link *linkPtr = event.get();
// First remove the link from the HOOMD bond table
int linkTag = linkPtr->tag();
boost::unordered_map<int, unsigned>::iterator it;
it = linkBondMap_.find(linkTag);
assert(it != linkBondMap_.end());
unsigned int oldBondTag = it ->second;
bondDataSPtr_->removeBond(oldBondTag);
// Add the modified link
// link type ids are mapped according to
// HOOMD bond id = nBondType + link type id
::Bond bond(simulation().nBondType()+linkPtr->typeId(),
linkPtr->atom0().id(),
linkPtr->atom1().id());
bondDataSPtr_->addBond(bond);
// Update link-bond mapping
unsigned int newBondTag = bondDataSPtr_->getLastTag();
it->second = newBondTag;
}
/**
* Remove a Link.
*/
void LinkMaster::removeLink(int id)
{
Link* linkPtr = &link(id);
int atom0Id;
int atom1Id;
if (!link(id).isActive()) {
UTIL_THROW("Attempt to remove a nonactive link");
}
atom0Id = linkPtr->atom0().id();
atom1Id = linkPtr->atom1().id();
// Remove link from atom0 and atom1 link sets
if (!atomLinkSets_[atom0Id].isElement(*linkPtr)) {
UTIL_THROW("Link is not in atomLinkSets of atom0");
}
if (!atomLinkSets_[atom1Id].isElement(*linkPtr)) {
UTIL_THROW("Link is not in atomLinkSets of atom1");
}
atomLinkSets_[atom0Id].remove(*linkPtr);
atomLinkSets_[atom1Id].remove(*linkPtr);
// Notify observers of removal of this Link.
// Notify before clearing Link so atomPtrs and typeId are available.
LinkRemoveEvent event(linkPtr);
Notifier<LinkRemoveEvent>::notifyObservers(event);
// Clear the link: nullify atomPtrs, set typeId = -1, isActive = false
linkPtr->clear();
// Return link to reservoir
linkSet_.remove(*linkPtr);
reservoir_.push(*linkPtr);
}
/*
* Modify one atom attached to a link
*/
void LinkMaster::reSetAtom(Link& link, Atom& atom, int endId)
{
int atomId = atom.id();
int oldAtomId;
if (endId==0){
oldAtomId = link.atom0().id();
}
else {
oldAtomId = link.atom1().id();
}
// Check preconditions
if (!link.isActive()) {
UTIL_THROW("Attempt to reset an atom for a nonactive link");
}
if (atomId < 0 || atomId >= atomCapacity_) {
Log::file() << "AtomId = " << atomId << std::endl;
Log::file() << "atomCapacity = " << atomCapacity_ << std::endl;
UTIL_THROW("Invalid atom id");
}
// Remove link from oldAtom link sets
if (!atomLinkSets_[oldAtomId].isElement(link)) {
UTIL_THROW("Link is not in atomLinkSets of atom");
}
atomLinkSets_[oldAtomId].remove(link);
// Change the atom
if (endId==0){
link.setAtoms(atom,link.atom1());
}
else {
link.setAtoms(link.atom0(),atom);
}
atomLinkSets_[atomId].append(link);
ReSetAtomEvent event(&link, endId);
Notifier<ReSetAtomEvent>::notifyObservers(event);
}
/*
* Modify the atoms attached to a link
*/
void LinkMaster::reSetAtoms(Link& link, Atom& atom0, Atom& atom1)
{
int atom0Id = atom0.id();
int atom1Id = atom1.id();
int oldAtom0Id = link.atom0().id();
int oldAtom1Id = link.atom1().id();
// Check preconditions
if (!link.isActive()) {
UTIL_THROW("Attempt to reset atoms for a nonactive link");
}
if (atom0Id < 0 || atom0Id >= atomCapacity_) {
Log::file() << "Atom0Id = " << atom0Id << std::endl;
Log::file() << "atomCapacity = " << atomCapacity_ << std::endl;
UTIL_THROW("Invalid atom0 id");
}
if (atom1Id < 0 || atom1Id >= atomCapacity_) {
Log::file() << "Atom1Id = " << atom1Id << std::endl;
Log::file() << "atomCapacity = " << atomCapacity_ << std::endl;
UTIL_THROW("Invalid atom1 id");
}
// Remove link from oldAtom0 and oldAtom1 link sets
if (!atomLinkSets_[oldAtom0Id].isElement(link)) {
UTIL_THROW("Link is not in atomLinkSets of atom0");
}
if (!atomLinkSets_[oldAtom1Id].isElement(link)) {
UTIL_THROW("Link is not in atomLinkSets of atom1");
}
atomLinkSets_[oldAtom0Id].remove(link);
atomLinkSets_[oldAtom1Id].remove(link);
// Change the atoms
link.setAtoms(atom0,atom1);
atomLinkSets_[atom0Id].append(link);
atomLinkSets_[atom1Id].append(link);
LinkResetEvent event(&link);
Notifier<LinkResetEvent>::notifyObservers(event);
}
/**
* connection to LinkAddEvent
*/
void HoomdMove::update(const LinkAddEvent& event)
{
if (!HoomdIsInitialized_) return;
// Add a link as a HOOMD bond
Link *linkPtr = event.get();
::Bond bond(simulation().nBondType()+linkPtr->typeId(),
linkPtr->atom0().id(),
linkPtr->atom1().id());
bondDataSPtr_->addBond(bond);
// keep track of bond
unsigned int bondTag = bondDataSPtr_->getLastTag();
int linkTag = linkPtr->tag();
#ifdef UTIL_DEBUG
std::pair<boost::unordered_map<int, unsigned int>::iterator,bool> ret;
ret=
#endif
linkBondMap_.insert(std::pair<int,unsigned int>(linkTag,bondTag));
assert(ret.second);
}
/*
* Write the configuration file.
*/
void McMdConfigIo::write(std::ostream &out)
{
using std::endl;
// Write Boundary dimensions
out << "BOUNDARY" << endl << endl;
out << boundary() << endl;
// Write atomic positions
System::ConstMoleculeIterator molIter;
Molecule::ConstAtomIterator atomIter;
Species* speciesPtr;
int iSpecies, iMolecule;
out << endl << "MOLECULES" << endl;
for (iSpecies = 0; iSpecies < simulation().nSpecies(); ++iSpecies) {
out << endl;
out << "species " << iSpecies << endl;
out << "nMolecule " << system().nMolecule(iSpecies) << endl;
speciesPtr = &simulation().species(iSpecies);
iMolecule = 0;
system().begin(iSpecies, molIter);
for ( ; molIter.notEnd(); ++molIter) {
out << endl;
out << "molecule " << iMolecule << endl;
if (speciesPtr->isMutable()) {
speciesPtr->mutator().writeMoleculeState(out, *molIter);
}
for (molIter->begin(atomIter); atomIter.notEnd(); ++atomIter) {
//out << atomIter->position() << endl;
writeAtom(out, *atomIter);
}
++iMolecule;
}
}
#ifdef INTER_TETHER
{ // Scope for local variables
// Write Tethers
Tether* tetherPtr;
Atom* atomPtr;
Molecule* molPtr;
int iTether, nTether, iAtom;
out << std::endl;
out << "TETHERS" << endl << endl;
nTether = system().tetherMaster().nTether();
out << Label("nTether") << nTether << std::endl;
for (iTether = 0; iTether < nTether; ++iTether) {
tetherPtr = &(system().tetherMaster().tether(iTether));
atomPtr = &tetherPtr->atom();
molPtr = &atomPtr->molecule();
iAtom = atomPtr->indexInMolecule();
iMolecule = system().moleculeId(*molPtr);
iSpecies = molPtr->species().id();
out << Int(iSpecies,5) << Int(iMolecule,9) << Int(iAtom,6)
<< tetherPtr->anchor() << std::endl;
}
}
#endif
#ifdef MCMD_LINK
{ // Scope for local variables
// Write Links
Link* linkPtr;
Atom* atomPtr;
Molecule* molPtr;
int iLink, nLink, iAtom;
out << std::endl;
out << "LINKS" << endl << endl;
nLink = system().linkMaster().nLink();
out << Label("nLink") << nLink << std::endl;
for (iLink = 0; iLink < nLink; ++iLink) {
linkPtr = &(system().linkMaster().link(iLink));
// Output species, molecule, atom ids for atom 0
atomPtr = &(linkPtr->atom0());
molPtr = &atomPtr->molecule();
iAtom = atomPtr->indexInMolecule();
iMolecule = system().moleculeId(*molPtr);
iSpecies = molPtr->species().id();
out << Int(iSpecies,8) << Int(iMolecule,8) << Int(iAtom,8);
out << " ";
// Output species, molecule, atom ids for atom 1
atomPtr = &(linkPtr->atom1());
molPtr = &atomPtr->molecule();
iAtom = atomPtr->indexInMolecule();
iMolecule = system().moleculeId(*molPtr);
iSpecies = molPtr->species().id();
out << Int(iSpecies,8) << Int(iMolecule,8) << Int(iAtom,8);
out << " ";
out << Int(linkPtr->typeId(),8) << std::endl;
}
}
#endif
}
// Create or destroy the slip-springs.
bool SliplinkerAll::move()
{
System::MoleculeIterator molIter;
Molecule::AtomIterator atomIter;
Atom *atom0Ptr, *atom1Ptr;
Atom* atomPtr;
Molecule *mol0Ptr, *mol1Ptr;
Molecule* molIPtr;
double prob, dRSq, mindRSq=cutoff_*cutoff_, rnd, norm;
int i, ntrials, j, nNeighbor, idLink, iAtom, id1, id0;
int iAtom0, iAtom1, iMolecule0, iMolecule1, n0;
Link* linkPtr;
static const int maxNeighbor = CellList::MaxNeighbor;
double cdf[maxNeighbor], energy, sum;
int idneighbors[maxNeighbor];
ntrials = 2 * system().simulation().atomCapacity();
for (i=0; i < ntrials; ++i){
//Choose to create or destroy a link with prob 0.5
if (random().uniform(0.0, 1.0) > 0.5){
// Try to create a link.
incrementNAttempt();
// Choose a molecule and atom at random
molIPtr = &(system().randomMolecule(speciesId_));
iMolecule0 = system().moleculeId(*molIPtr);
iAtom = random().uniformInt(0, molIPtr->nAtom());
atomPtr = &molIPtr->atom(iAtom);
id0 = atomPtr->id();
// Get array of neighbors
system().pairPotential().cellList().getNeighbors(atomPtr->position(), neighbors_);
nNeighbor = neighbors_.size();
n0 = 0;
sum = 0;
// Loop over neighboring atoms
for (j = 0; j < nNeighbor; ++j) {
atom1Ptr = neighbors_[j];
mol1Ptr = &atom1Ptr->molecule();
iMolecule1 = system().moleculeId(*mol1Ptr);
id1 = atom1Ptr->id();
// Check if atoms are the same
if (id0 != id1){
// Exclude masked pairs
if (!atomPtr->mask().isMasked(*atom1Ptr)) {
// Identify possible partners and calculate the cumulative distribution function
dRSq = system().boundary().distanceSq(atomPtr->position(), atom1Ptr->position());
if (dRSq <= mindRSq) {
energy = system().linkPotential().energy(dRSq, 0);
//energy = 0.5*dRSq;
sum = sum + boltzmann(energy);
cdf[n0] = sum;
idneighbors[n0] = j;
n0++;
}
}
}
}
// If at least 1 candidate has been found.
if (n0 > 0) {
// Choose a partner with probability cdf[j]/cdf[n0-1]
j = 0;
rnd = random().uniform(0.0, 1.0);
norm = 1.0/cdf[n0-1];
while (rnd > cdf[j]*norm ){
j = j + 1;
}
atom1Ptr = neighbors_[idneighbors[j]];
// Create a slip-link between the selected atoms with probability = prob
prob = 2.0 * (system().linkMaster().nLink() + 1.0);
prob = system().simulation().atomCapacity() * boltzmann(-mu_) * cdf[n0-1]/ prob ;
//prob = 2.0 * system().nMolecule(speciesId_) * boltzmann(-mu_) * cdf[n0-1]/ prob ;
if (system().simulation().random().uniform(0.0, 1.0) < prob) {
system().linkMaster().addLink(*atomPtr, *atom1Ptr, 0);
incrementNAccept();
}
}
}
else {
// Try to destroy a link
incrementNAttempt();
// Choose a link at random
if (system().linkMaster().nLink() > 0){
idLink = random().uniformInt(0, system().linkMaster().nLink());
// Indentify the atoms for this link.
linkPtr = &(system().linkMaster().link(idLink));
atom0Ptr = &(linkPtr->atom0());
mol0Ptr = &atom0Ptr->molecule();
iMolecule0 = system().moleculeId(*mol0Ptr);
iAtom0 = atom0Ptr->indexInMolecule();
atom1Ptr = &(linkPtr->atom1());
mol1Ptr = &atom1Ptr->molecule();
iMolecule1 = system().moleculeId(*mol1Ptr);
iAtom1 = atom1Ptr->indexInMolecule();
// try to delete the slip-spring
dRSq = system().boundary().distanceSq(atom0Ptr->position(), atom1Ptr->position());
// try to delete the link if the bond is smaller than the cutoff
if (dRSq <= mindRSq) {
// Get array of neighbors
system().pairPotential().cellList().getNeighbors(atom0Ptr->position(), neighbors_);
nNeighbor = neighbors_.size();
id0 = atom0Ptr->id();
n0 = 0;
sum = 0;
// Loop over neighboring atoms
for (j = 0; j < nNeighbor; ++j) {
atom1Ptr = neighbors_[j];
mol1Ptr = &atom1Ptr->molecule();
iMolecule1 = system().moleculeId(*mol1Ptr);
id1 = atom1Ptr->id();
// Check if atoms are the same
if (id0 != id1){
// Exclude masked pairs
if (!atom0Ptr->mask().isMasked(*atom1Ptr)) {
// Identify possible partners and calculate the cumulative distribution function
dRSq = system().boundary().distanceSq(atom0Ptr->position(), atom1Ptr->position());
if (dRSq <= mindRSq) {
energy = system().linkPotential().energy(dRSq, 0);
//energy = 0.5*dRSq;
sum = sum + boltzmann(energy);
cdf[n0] = sum;
idneighbors[n0] = j;
n0++;
}
}
}
}
// Destroy the slip-link between the selected atoms with probability = prob
//prob = 2.0 * system().nMolecule(speciesId_) * boltzmann(-mu_) * cdf[n0-1];
prob = system().simulation().atomCapacity() * boltzmann(-mu_) * cdf[n0-1];
prob = 2.0 * system().linkMaster().nLink() / prob;
if (system().simulation().random().uniform(0.0, 1.0) < prob) {
system().linkMaster().removeLink(idLink);
incrementNAccept();
}
}
}
}
}
return true;
}
