void AtomicCompositionTable::CreateAtomicElementLists(const SpeciesMap& species)
{
// Recover atomic elements
for(unsigned int i=0;i<species.size();i++)
{
OpenSMOKE::AtomicComposition atomic;
species[i].AtomicComposition(&atomic);
for(unsigned int k=0;k<atomic.element_names().size();k++)
{
bool iFound = false;
for(unsigned int j=0;j<element_names_list_.size();j++)
if ( atomic.element_names()[k] == element_names_list_[j] )
{
iFound = true;
break;
}
if (iFound == false)
element_names_list_.push_back(atomic.element_names()[k]);
}
}
// Recover atomic weights
element_weights_list_.resize(element_names_list_.size());
element_weights_list_.setZero();
for(unsigned int j=0;j<element_names_list_.size();j++)
element_weights_list_(j) = OpenSMOKE::AtomicWeights[element_names_list_[j]];
// Recover atomic elements
element_coefficients_list_.resize(species.size(), element_names_list_.size());
element_coefficients_list_.setZero();
for(unsigned int i=0;i<species.size();i++)
{
OpenSMOKE::AtomicComposition atomic;
species[i].AtomicComposition(&atomic);
for(unsigned int k=0;k<atomic.element_names().size();k++)
{
bool iFound = false;
for(unsigned int j=0;j<element_names_list_.size();j++)
if ( atomic.element_names()[k] == element_names_list_[j] )
{
element_coefficients_list_(i,j) = atomic.element_coefficients()[k];
break;
}
}
}
}
void AtomicCompositionTable::CreateAtomicElementLists(const SpeciesMap& species)
{
// Recover atomic elements
for(unsigned int i=0;i<species.size();i++)
{
OpenSMOKE::AtomicComposition atomic;
species[i].AtomicComposition(&atomic);
for(unsigned int k=0;k<atomic.element_names().size();k++)
{
bool iFound = false;
for(unsigned int j=0;j<element_names_list_.size();j++)
if ( atomic.element_names()[k] == element_names_list_[j] )
{
iFound = true;
break;
}
if (iFound == false)
element_names_list_.push_back(atomic.element_names()[k]);
}
}
// Reorder
{
unsigned current_index = 0;
std::vector<std::string> target_elements = { "C", "H", "O", "N" };
for (unsigned int k = 0; k < target_elements.size(); k++)
{
for (unsigned int j = 0; j < element_names_list_.size(); j++)
if (element_names_list_[j] == target_elements[k])
{
std::iter_swap(element_names_list_.begin() + current_index, element_names_list_.begin() + j);
current_index++;
break;
}
}
}
// Recover atomic weights
element_weights_list_.resize(element_names_list_.size());
element_weights_list_.setZero();
for(unsigned int j=0;j<element_names_list_.size();j++)
element_weights_list_(j) = OpenSMOKE::AtomicWeights[element_names_list_[j]];
// Recover atomic elements
element_coefficients_list_.resize(species.size(), element_names_list_.size());
element_coefficients_list_.setZero();
for(unsigned int i=0;i<species.size();i++)
{
OpenSMOKE::AtomicComposition atomic;
species[i].AtomicComposition(&atomic);
for(unsigned int k=0;k<atomic.element_names().size();k++)
{
bool iFound = false;
for(unsigned int j=0;j<element_names_list_.size();j++)
if ( atomic.element_names()[k] == element_names_list_[j] )
{
element_coefficients_list_(i,j) = atomic.element_coefficients()[k];
break;
}
}
}
}
bool Species::IsGoingExtinct() {
return (m_fitness < 0.0 && m_incomingInteractions.size() > 0);
}
void Species::MakeInteractionWith(Species* other, double coefficient) {
m_incomingInteractions.insert( std::make_pair(other, coefficient) );
m_fitness += coefficient;
other->m_outgoingInteractions.insert(this);
other->m_cacheReady = false;
}
size_t Species::InDegree() const {
return m_incomingInteractions.size();
}