void SpecialAgentAccumulateDataAction::fire(Data *d) {
// cerr << "# inside specialAgentAccumulatedata" << endl;
if (this->agent == NULL)
throw HiveException("action was not assigned to an agent", "SpecialAgentAccumulateDataAction::fire(Data *d)");
if (d->getType().compare("tvectordata_double")!=0)
throw HiveException("wrong data passed to action", "SpecialAgentAccumulateDataAction::fire(Data *d)");
// cerr << "INSIDE SPECIALAGENT FIRE" << endl;
// convert data argument into correct format
TVectorData<double> *c = (TVectorData<double> *) d;
// get the databases from the agent ... do we really need the meta database ?! not really
// one could do without ... i just thought it would be funny to have a meta database in a special agent
// called fox mulder ... but i guess that we should remove this ...
Database *meta = ((SpecialAgent *) agent)->getMetaDatabase();
Database *db = agent->getDatabase();
// get some meta information
IntegerData *num_adds = (IntegerData* ) meta->getDataItem("number_of_adds");
IntegerData *num_cells = (IntegerData* ) meta->getDataItem("total_number_of_cells");
IntegerData *num_time_steps_between_outputs = (IntegerData* ) meta->getDataItem("number_between_outputs");
IntegerData *counter = (IntegerData* ) meta->getDataItem("counter");
// accumulate the data
if (num_adds->getInteger() == 0) {
// fill data
TVectorData<double> *conc = (TVectorData<double> *) db->getDataItem("total_conc");
for (int i=1; i<c->size(); i++)
conc->at(i-1) = c->at(i);
} else {
TVectorData<double> *conc = (TVectorData<double>*) db->getDataItem("total_conc");
for (int i=1; i<c->size(); i++)
conc->at(i-1) = conc->at(i-1) + c->at(i);
}
num_adds->setInteger(num_adds->getInteger()+1);
// check whether output has to be generated
if (num_adds->getInteger() == num_cells->getInteger() &&
counter->getInteger() == num_time_steps_between_outputs->getInteger()-1) {
// cerr << "JETZT BIN ICH HIER DIRIN UND SOLLTE ETWAS AUSGEBEN!!!" << endl;
TVectorData<double> *conc = (TVectorData<double>*) db->getDataItem("total_conc");
DoubleData *gt = (DoubleData* ) meta->getDataItem("global_time");
DoubleData *dt = (DoubleData* ) meta->getDataItem("time_step");
// output time;
*this->out << setw(12) << setfill(' ') << gt->getDouble()*num_time_steps_between_outputs->getInteger();
// update time
gt->setDouble(gt->getDouble() + dt->getDouble());
// output conc vector
for (int i=0; i<conc->size(); i++)
*this->out << setw(12) << setfill(' ') << conc->at(i)/num_cells->getInteger();
*this->out << endl;
// reset num_adds
num_adds->setInteger(0);
// reset counter
counter->setInteger(0);
} else if (num_adds->getInteger() == num_cells->getInteger()){
// cerr << "hier drin" << endl;
num_adds->setInteger(0);
counter->setInteger(counter->getInteger()+1);
}
}
void MassBalance::step(double dt) {
IntegerVectorData* agBoundaryIndecies = (IntegerVectorData*)this->getDataFromAgent(this->boundaryIndecies);
DoubleVectorData* agBoundaryArray = (DoubleVectorData*)this->getDataFromAgent(this->boundaryArray);
DoubleVectorData* agSubstrateConcentrationArray = (DoubleVectorData*)this->getDataFromAgent(this->substrateConcentrationArray);
DoubleData* agCellVolume = (DoubleData*)this->getDataFromAgent(this->cellVolume);
for (int i=0; i < agBoundaryIndecies->getNumElements(); i++) {
double conc = agSubstrateConcentrationArray->getDouble(agBoundaryIndecies->getInteger(i));
conc = (agCellVolume->getDouble()*conc+agBoundaryArray->getDouble(i))/agCellVolume->getDouble();
agSubstrateConcentrationArray->setDouble(conc,agBoundaryIndecies->getInteger(i));
}
}
void UpdateLigandConcentration::fire (Data *d) {
// do the correct cast of the data
DoubleData *conc = (DoubleData *) d;
DoubleData *ligand = (DoubleData *) agent->getDatabase()->getDataItem("LigandConcentration");
ligand->setDouble(conc->getDouble());
}
void CellNotifyLigandConcToNFsimMessageGenerator::placeMessage(int destID) {
Message *msg = new Message();
msg->setAction(ChemotaxisActionIDs::UPDATE_LIGAND_CONCENTRATION_ACTION_ID);
msg->setDestinationID(destID);
// provide argument for message
DoubleData *parameter = new DoubleData("ligand_concentration", 0);
// get chemicals out of cells database
//if(this->db->existsDataItem("Chemical")) cout<<"got it chief"<<endl;
//else cout<<"nopers"<<endl;
DoubleVectorData *chem = (DoubleVectorData*) this->db->getDataItem("Chemical");
parameter->setDouble(chem->getDouble(0));
cerr << "i am the cell and i am sending " << parameter->getDouble() << " as lig. to nfsim" << endl;
// get the chemoattractant
msg->setArgument(parameter);
// place message
source->placeMessageInOutbox(msg);
}
void BlindAgentNotifyWorldThatNewAgentIsBorn::placeMessage(int destID) {
//check if I have to give birth or not
if(birthFlag->getBool())
{
birthFlag->setBool(false);
// if the death simulator determined death, then do not create the birth message
if(deathFlag->getBool()) return;
//get the agentfactory, and use it to create an agent
AgentFactory *af = Registrar::getSystemRegistrar()->getAgentFactory(1);
Agent *a = af->createAgent();
// has the same parent
// NOTE: the parent is the top level agent in the hierarchy of agents,
// not the agent that gave birth!
a->setParent(source->getParentId());
// has the same special agents
for(unsigned int s=0; s<source->getNumOfSpecialAgents(); s++)
a->addSpecialAgent(source->getSpecialAgentId(s));
// needs the same communicator, of course, of course
a->addCommunicator(source->getCommunicator());
// set the other properties of agent 'a' based on the source exactly...
a->copyDatabaseInformationFromExistingAgent(this->source);
// CLEARLY A HACK!! CHANGE THIS AT SOME POINT TO DUPLICATE SIMULATORS
// replace the movement simulator with the correct one
if (((BoolData*) a->getDatabase()->getDataItem("is_levy"))->getBool()) {
LevyRunLengthSimulator *levy = new LevyRunLengthSimulator();
a->replaceSimulator(0,levy);
} else {
ExponentialRunLengthSimulator *expo = new ExponentialRunLengthSimulator();
a->replaceSimulator(0,expo);
}
// ANOTHER HACK !! TIME TO NEXT OUTPUT IS OFF WHEN WE GET HERE, SO WE MUST UPDATE
DoubleData *t = (DoubleData *) a->getDatabase()->getDataItem("celltime");
//DoubleData *oi = (DoubleData *) a->getDatabase()->getDataItem("outputinterval");
//DoubleData *no = (DoubleData*) a->getDatabase()->getDataItem("nextOutputTime");
DoubleData *dt = (DoubleData *) a->getDatabase()->getDataItem("dt");
t->setDouble(t->getDouble()-dt->getDouble());
//register agent a
Message *specialMssg = new Message();
specialMssg->setAction(ChemoPopActionIDs::SPECIAL_AGENT_UPDATE_BLIND_AGENT_COUNT_ACTION_ID);
specialMssg->setArgument(new IntegerData("ChangeInBlindAgentNumber",1));
Registrar::getSystemRegistrar()->registerNewAgentAndSendMessageToSpecialAgent(a,specialMssg);
// Now, send the message to the world!!
Message *msg = new Message();
msg->setAction(ChemoPopActionIDs::UPDATE_WORLD_BLIND_AGENT_BIRTH_ACTION_ID);
msg->setDestinationID(destID);
//pass my agentID (the mother) and the new agent ID (the baby)
TVectorData<int> *info = new TVectorData<int>("new_cell_info","tvectordata_int");
info->addElementToEnd(this->source->getAgentId());
info->addElementToEnd(a->getAgentId()); // get new AgentID !!!
msg->setArgument(info);
source->placeMessageInOutbox(msg);
}
}