// calculator
void CoordinationBase::calculate()
{
double ncoord=0.;
Tensor virial;
vector<Vector> deriv(getNumberOfAtoms());
// deriv.resize(getPositions().size());
if(nl->getStride()>0 && invalidateList){
nl->update(getPositions());
}
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if(serial){
stride=1;
rank=0;
}else{
stride=comm.Get_size();
rank=comm.Get_rank();
}
for(unsigned int i=rank;i<nl->size();i+=stride) { // sum over close pairs
Vector distance;
unsigned i0=nl->getClosePair(i).first;
unsigned i1=nl->getClosePair(i).second;
if(getAbsoluteIndex(i0)==getAbsoluteIndex(i1)) continue;
if(pbc){
distance=pbcDistance(getPosition(i0),getPosition(i1));
} else {
distance=delta(getPosition(i0),getPosition(i1));
}
double dfunc=0.;
ncoord += pairing(distance.modulo2(), dfunc,i0,i1);
deriv[i0] = deriv[i0] + (-dfunc)*distance ;
deriv[i1] = deriv[i1] + dfunc*distance ;
virial=virial+(-dfunc)*Tensor(distance,distance);
}
if(!serial){
comm.Sum(ncoord);
if(!deriv.empty()) comm.Sum(&deriv[0][0],3*deriv.size());
comm.Sum(virial);
}
for(unsigned i=0;i<deriv.size();++i) setAtomsDerivatives(i,deriv[i]);
setValue (ncoord);
setBoxDerivatives (virial);
}
std::string Mapping::getArgumentName( unsigned& iarg ){
if( iarg < getNumberOfArguments() ) return getPntrToArgument(iarg)->getName();
unsigned iatom=iarg - getNumberOfArguments();
std::string atnum; Tools::convert( getAbsoluteIndex(iatom).serial(),atnum);
unsigned icomp=iatom%3;
if(icomp==0) return "pos" + atnum + "x";
if(icomp==1) return "pos" + atnum + "y";
return "pos" + atnum + "z";
}
void VectorPortBit::getConnectedNets(std::vector<NetSharedPtr>& outNets,
bool inSkipChildConnections) const throw (Error) {
//First get connections exclusive to me
Port::getConnectedNets(outNets);
//Append cousins from nets that have been connected to my
//parent
if(!inSkipChildConnections) {
VectorBit<Net>::List parentConnections;
Composite<Port>::Pointer parent = getParentCollection();
if(!parent) {
Error e(eMessageIdErrorPointerToItemDoesNotExist, __FUNCTION__, __FILE__, __LINE__);
e.saveContextData("Pointer to parent collection does not exist", parent);
throw e;
}
if(eCompositionTypeVector != parent->getCompositionType()) {
Error e(eMessageIdErrorCompositionTypeMismatch, __FUNCTION__, __FILE__, __LINE__);
e.saveContextData("Composition type mismatch", parent->getCompositionType());
throw e;
}
parent->getConnectedNets(parentConnections, true);
VectorBit<Net>::List::iterator connNet = parentConnections.begin();
VectorBit<Net>::List::iterator connNetEnd = parentConnections.end();
const std::vector<VectorBit<Net>::SizeType>& myIndex = getIndices();
for(; connNet != connNetEnd; ++connNet) {
Composite<Net>::Pointer cousin;
if(eCompositionTypeVector == (*connNet)->getCompositionType()) {
cousin = (*connNet)->get(myIndex);
//We don't want to mess up preservervation
//by calling getChildren()
} else //Must be a bundle
{
VectorBit<Net>::List bChildren;
(*connNet)->getChildren(bChildren);
cousin = bChildren[getAbsoluteIndex()];
//We assume list is a vector
}
if(!cousin) {
Error e(eMessageIdErrorPointerToItemDoesNotExist, __FUNCTION__, __FILE__, __LINE__);
e.saveContextData("Pointer to item does not exist", cousin);
throw e;
}
outNets.push_back(cousin);
}
}
return;
}
// calculator
void CoordinationBase::calculate()
{
double ncoord=0.;
Tensor virial;
vector<Vector> deriv(getNumberOfAtoms());
// deriv.resize(getPositions().size());
if(nl->getStride()>0 && invalidateList) {
nl->update(getPositions());
}
unsigned stride=comm.Get_size();
unsigned rank=comm.Get_rank();
if(serial) {
stride=1;
rank=0;
} else {
stride=comm.Get_size();
rank=comm.Get_rank();
}
unsigned nt=OpenMP::getNumThreads();
const unsigned nn=nl->size();
if(nt*stride*10>nn) nt=nn/stride/10;
if(nt==0)nt=1;
#pragma omp parallel num_threads(nt)
{
std::vector<Vector> omp_deriv(getPositions().size());
Tensor omp_virial;
#pragma omp for reduction(+:ncoord) nowait
for(unsigned int i=rank; i<nn; i+=stride) {
Vector distance;
unsigned i0=nl->getClosePair(i).first;
unsigned i1=nl->getClosePair(i).second;
if(getAbsoluteIndex(i0)==getAbsoluteIndex(i1)) continue;
if(pbc) {
distance=pbcDistance(getPosition(i0),getPosition(i1));
} else {
distance=delta(getPosition(i0),getPosition(i1));
}
double dfunc=0.;
ncoord += pairing(distance.modulo2(), dfunc,i0,i1);
Vector dd(dfunc*distance);
Tensor vv(dd,distance);
if(nt>1) {
omp_deriv[i0]-=dd;
omp_deriv[i1]+=dd;
omp_virial-=vv;
} else {
deriv[i0]-=dd;
deriv[i1]+=dd;
virial-=vv;
}
}
#pragma omp critical
if(nt>1) {
for(int i=0; i<getPositions().size(); i++) deriv[i]+=omp_deriv[i];
virial+=omp_virial;
}
}
if(!serial) {
comm.Sum(ncoord);
if(!deriv.empty()) comm.Sum(&deriv[0][0],3*deriv.size());
comm.Sum(virial);
}
for(unsigned i=0; i<deriv.size(); ++i) setAtomsDerivatives(i,deriv[i]);
setValue (ncoord);
setBoxDerivatives (virial);
}