void ContributionScalarPluginFunction<Driver,PluginType>::doEvaluation()
{
List<scalarField> values(Pstream::nProcs());
values[Pstream::myProcNo()]=values_();
List<vectorField> positions(Pstream::nProcs());
positions[Pstream::myProcNo()]=positions_();
Pstream::scatterList(values);
Pstream::scatterList(positions);
typedef typename PluginType::driverType PluginTypeDriverType;
scalarField result(
this->parentDriver().size()
);
autoPtr<vectorField> myPositions(
makeParentPositions(
dynamicCast<PluginTypeDriverType &>(
this->parentDriver()
)
).ptr()
);
forAll(result,cellI)
{
scalar sum=0;
scalar distSum=0;
bool found=false;
const vector &here=myPositions()[cellI];
forAll(values,valI)
{
const scalarField &localValues=values[valI];
const vectorField &localPos=positions[valI];
forAll(localValues,i)
{
const scalar dist=mag(localPos[i]-here);
if(dist<SMALL) {
// Avoid divison by zero
result[cellI]=localValues[i];
found=true;
break;
}
// const scalar weight=dist*dist;
const scalar weight=dist;
sum+=localValues[i]/weight;
distSum+=1/weight;
}
if(found) {
break;
}
}
if(!found) {
result[cellI]=sum/distSum;
}
}
void MoleculeGroup::WriteGro(const std::string& gro, const arma::rowvec& box,
const std::string description) {
std::ofstream gro_file;
gro_file.open(gro.c_str());
assert(gro_file.is_open());
gro_file << description << std::endl;
gro_file << group_size_ << std::endl;
for (int i_atom = 0; i_atom < group_size_; i_atom++) {
gro_file << boost::format("%5d%-5s%5s%5d%8.3f%8.3f%8.3f%8.4f%8.4f%8.4f") %
(index_to_molecular_index_[i_atom]+1) %
molecule_name(index_to_molecular_index_[i_atom]) %
atom_name(i_atom) % (indices_[i_atom]+1) % positions_(i_atom,0) %
positions_(i_atom,1) % positions_(i_atom,2) %
velocities_(i_atom,0) % velocities_(i_atom,1) %
velocities_(i_atom,2) << std::endl;
}
gro_file << boost::format("%10.5f%10.5f%10.5f") % box(0) % box(1) % box(2);
gro_file.close();
}
inline double position(int atom, int dim) const {
return positions_(atom, dim);
}
