//Do the reaction A + B -> C + D. So that A <- C and B <- D.
//We need to consider that the source molecule can be either A or B.
//If A and C belong to the same compartment, A <- C.
//Otherwise, find a vacant adjoining voxel of A, X which is the same compartment
//as C and X <- C.
//Similarly, if B and D belong to the same compartment, B <- D.
//Otherwise, find a vacant adjoining voxel of C, Y which is the same compartment
//as D and Y <- D.
//We need to consider that the source molecule can be either A or B.
bool PolymerizationProcess::react(Voxel* moleculeB, Voxel** target)
{
Voxel* moleculeA(*target);
//moleculeA is the source molecule. It will be soft-removed (id kept intact)
//by the calling Species if this method returns true.
//moleculeB is the target molecule, it will also be soft-removed by the
//calling Species.
//First let us make sure moleculeA and moleculeB belong to the
//correct species.
if(moleculeA->id != A->getID())
{
Voxel* tempA(moleculeA);
moleculeA = moleculeB;
moleculeB = tempA;
}
//C && D must be protomers:
if(C && D)
{
//Dimerization reaction:
if(!A->getIsPolymer() && !B->getIsPolymer())
{
initSubunit(moleculeA, C);
Subunit* subunitA(moleculeA->subunit);
Voxel* moleculeD(getTargetVoxel(subunitA));
if(moleculeD != NULL &&
(moleculeD == moleculeB ||
theSpatiocyteStepper->id2species(moleculeD->id)->getIsLipid()))
{
moleculeB->id = B->getVacantID();
initJoinSubunit(moleculeD, D, subunitA);
moleculeD->subunit->sourceVoxels[theBendIndexB] = moleculeA;
C->addMolecule(moleculeA);
updateSharedLipidsID(moleculeA);
D->addMolecule(moleculeD);
//add bends for SpatiocyteNextReactionProcess
finalizeReaction();
return true;
}
resetSubunit(subunitA);
}
//Polymer elongation reaction:
//A is the reference polymer subunit:
else if(A->getIsPolymer() && !B->getIsPolymer())
{
//Make sure the moleculeA is not a shared molecule by updating
//it to the actual molecule pointed by the subunit.
//It can be a shared molecule if it is not the source molecule.
moleculeA = moleculeA->subunit->voxel;
Subunit* subunitA(moleculeA->subunit);
Voxel* moleculeD(subunitA->targetVoxels[theBendIndexA]);
if(moleculeD == NULL)
{
moleculeD = getTargetVoxel(subunitA);
}
if(moleculeD != NULL &&
(moleculeD == moleculeB || theSpatiocyteStepper->id2species(
moleculeD->id)->getIsLipid()))
{
moleculeB->id = B->getVacantID();
initJoinSubunit(moleculeD, D, subunitA);
moleculeD->subunit->sourceVoxels[theBendIndexB] = moleculeA;
C->addMolecule(moleculeA);
updateSharedLipidsID(moleculeA);
D->addMolecule(moleculeD);
//add bends for SpatiocyteNextReactionProcess
finalizeReaction();
return true;
}
}
}
//Single product polymerization:
else
{
//Depolymerize once react:
if(A->getIsPolymer() && !B->getIsPolymer() && !C->getIsPolymer())
{
Voxel* moleculeC;
if(A->getVacantID() != C->getVacantID())
{
if(B->getVacantID() != C->getVacantID())
{
moleculeC = C->getRandomAdjoiningVoxel(moleculeA,
SearchVacant);
if(moleculeC == NULL)
{
moleculeC = C-> getRandomAdjoiningVoxel(moleculeB,
SearchVacant);
if(moleculeC == NULL)
{
//cout << "unavailable" << endl;
return false;
}
}
}
else
{
moleculeC = moleculeB;
}
}
else
{
moleculeC = moleculeA;
}
moleculeA->id = A->getVacantID();
moleculeB->id = B->getVacantID();
C->addMolecule(moleculeC);
resetSubunit(moleculeA->subunit);
finalizeReaction();
//cout << "left" << endl;
return true;
}
}
return false;
}
ScenarioResult * ScenarioProblem::simProblem(){
ScenarioResult * sr = new ScenarioResult(_pd);
int seed = _pd->getSeed() + _scenario*100000 + _trial*33000;
int subSeed;
if(!_pd->getSubProblemGenerated()){
_simSP.generateSubProblem(0,_pd,_scenario);
}
// IloEnv env;
// _pd->setEnv(env);
IloEnv env = _pd->getEnv();
IloModel mod(env);
addSimProblem(mod);
try
{
IloCplex cplex(mod);
cplex.setOut(env.getNullStream());
Tree<Node> ref;
ref.buildTree( _pd->getOutcomes(), _pd->getStages());
Grid* g = _pd->getGrid();
int E = _pd->getGrid()->getBranchSize();
int V = _pd->getGrid()->getBusSize();
IloNum temp;
IloNumArray tempA(env);
IloNumArray tempB(env);
double R;
double L = _pd->getEffectiveDistribution();
double U;
double f;
double fabs;
double alpha;
double x;
int parent;
double tempCount;
int isDone;
//fix x variables
for(int j=0;j<E; j++){
_simSP.setOutage(j, false);
}
//add outages
for(int j=0; j<_pd->getNumberOutages(_scenario) ; j++){
_simSP.setOutage(_pd->getOutages(_scenario,j), true);
}
for(int i=0;i<ref.getSize();i++){
subSeed = seed + i*1000;
parent= ref[i]->getParent();
if( i!= 0 && _pd->getEnergyStorage() ){//storage logic
//cout<<"\ni:"<<i<<",pnt:"<<parent<<",es:"<<sr->getETotal(parent);
for(int j=0; j<V; j++){
_simSP.setPriorES(j, sr->getE( parent, j ) );
}
}
if( i!=0 ) isDone = (int)sr->getDone( parent );
else isDone = 0;
if( isDone ){
sr->updateDone(i, 1);
sr->updateDTotal(i,sr->getDTotal(parent));
sr->updatePDeltaTotal(i,0);
sr->updateXTotal(i,sr->getXTotal(parent));
}
else{
tempCount=0;
for(int j=0; j<E; j++){ //set branch outages
if( i!=0) {
//OUTAGE LOGIC if not root node
x = sr->getX(parent,j);
if( x == 0 ){ //branch not out
srand(subSeed + j);
alpha = rand() / double(RAND_MAX); //uniform 0-1
U = g->getBranchCapacity(j);
R = L + (1-L)*alpha;
R = R*U;
alpha = rand() / double(RAND_MAX); //uniform 0-1
if ( alpha > _pd->getProbability() ) R = U + 1;
f = sr->getF(parent,j);
if( f > 0 ) fabs = f;
else fabs = -f;
//outage branches
if( fabs > R) {
_simSP.setOutage(j,true);
tempCount += 1;
}
else _simSP.setOutage(j,false);
}
else{
_simSP.setOutage(j,true);
}
}
}
if(tempCount>0) sr->updateDone(i,0);
else if(tempCount==0 && i != 0) sr->updateDone(i,1);
else sr->updateDone(i,0);
if(cplex.solve()){
// temp = cplex.getObjValue();
temp = cplex.getValue( _simSP.getSumD() );
sr->updateDTotal(i,temp);
cplex.getValues(tempA, _simSP.getD() );
tempCount=0;
for(int j=0; j<V; j++){
sr->updateD(i, j,tempA[j]); //bus injects
}
cplex.getValues(tempA, _simSP.getP() );
tempCount=0;
for(int j=0; j<V; j++){
sr->updateP(i, j,tempA[j]); //bus injects
if( i!=0 ){
temp = tempA[j];
temp -= sr->getP( parent, j);
sr->updatePDelta(i,j,temp);
if(temp < 0) tempCount -= 0;//temp;
else tempCount += temp;
}
}
sr->updatePDeltaTotal(i,tempCount);
cplex.getValues(tempA, _simSP.getF() );
for(int j=0; j<E; j++){
sr->updateF(i,j, tempA[j]); //branch flows
}
cplex.getValues(tempA, _simSP.getX() );
tempCount=0;
for(int j=0; j<E; j++){
sr->updateX(i,j, tempA[j]); //branch flows
tempCount+= tempA[j];
}
sr->updateXTotal(i,tempCount);
if(_pd->getEnergyStorage() ){
cplex.getValues(tempA, _simSP.getE() );
for(int j=0; j<V; j++){
sr->updateE(i,j, tempA[j]); //branch flows
}
temp = cplex.getValue( IloSum(_simSP.getEDeltaPlus() ) );
sr->updateEDeltaPlus(i, temp);
temp = cplex.getValue( IloSum(_simSP.getEDeltaMinus() ) );
sr->updateEDeltaMinus(i, temp);
temp = cplex.getValue( IloSum(_simSP.getE() ) );
sr->updateETotal(i, temp);
}
}
}
}
// mod.end();
// env.end();
}
catch (IloException e)
{
cout << "An exception occurred. Exception Nr. " << e << endl;
}
return sr;
}
void mexFunction(int nlhs,mxArray* plhs[],int rhs,const mxArray* prhs[]) {
double A[] = {1,2,3,3,5,6,9,8,9};
Amatrix tempA(3, 3, A, false);
}
