void DumpSystem::dumpHeaderFile(double dumpTime) {
string dumpFileName = pathToFolder + s->getName()+"_nf."+Util::toString(dumpTime)+".dump.head";
//cout<<"writing file: "<<dumpFileName<<endl;;
ofstream ofs;
//ios_base::out -- Set for output only, instead of for input/output
//ios_base::trunc -- Truncate the file - that is overwrite anything that was already there
ofs.open((dumpFileName).c_str(), ios_base::out | ios_base::trunc);
//Make sure we could open the stream (this is really the only thing that can go around)
if(!ofs.is_open()) {
cout<<"--------"<<endl;
cout<<"-Error dumping header file.";
cout<<"-Could not open stream to file: '"<<dumpFileName<<"'"<<endl;
cout<<"-The path is probably incorrect or does not exist."<<endl;
return;
}
ofs<<"## Automatically generated file from NFsim. Do not edit manually.\n";
ofs<<"## To read this file and the associated information, use the\n";
ofs<<"## included Matlab script readNFdump.m.\n\n";
ofs<<"\n>> Time #######################################\n";
ofs<<dumpTime<<"\n";
ofs<<"\n>> MoleculeTypeDef ############################\n";
ofs<<"##\tindex\tname\tnumOfInstances\tnumOfComponents\n";
for(int i=0; i<s->getNumOfMoleculeTypes(); i++) {
MoleculeType *mt = s->getMoleculeType(i);
ofs<<"\t"<<i<<"\t"<<mt->getName()<<"\t"<<mt->getMoleculeCount()<<"\t";
ofs<<mt->getNumOfComponents()<<"\t"<<mt->getNumOfTypeIFunctions()<<"\n";
}
ofs<<"\n>> MoleculeTypeComponents #####################\n";
ofs<<"##\ttype\tindex\tname\n";
for(int i=0; i<s->getNumOfMoleculeTypes(); i++) {
MoleculeType *mt = s->getMoleculeType(i);
for(int k=0; k<mt->getNumOfComponents(); k++) {
ofs<<"\t"<<i<<"\t"<<k<<"\t"<<mt->getComponentName(k)<<"\n";
}
}
ofs<<"\n>> MoleculeTypeFunctions ######################\n";
ofs<<"##\ttype\tindex\tname\n";
for(int i=0; i<s->getNumOfMoleculeTypes(); i++) {
MoleculeType *mt = s->getMoleculeType(i);
for(int k=0; k<mt->getNumOfTypeIFunctions(); k++) {
ofs<<"\t"<<i<<"\t"<<k<<"\t"<<mt->getTypeILocalFunction(k)->getName()<<"\n";
}
}
ofs<<"\n>> EOF ##########################################\n";
ofs.flush();
ofs.close();
}
void DumpSystem::dumpMoleculeTypeFiles(double dumpTime) {
double complexCount = 0;
for(int i=0; i<s->getNumOfMoleculeTypes(); i++) {
MoleculeType *mt = s->getMoleculeType(i);
string dumpFileName = pathToFolder+s->getName() + "_nf."+Util::toString(dumpTime)+".dump."+Util::toString(i);
ofstream ofs;
//ios_base::out -- Set for output only, instead of for input/output
//ios_base::binary -- Set output to binary
//ios_base::trunc -- Truncate the file - that is overwrite anything that was already there
ofs.open((dumpFileName).c_str(), ios_base::out | ios_base::binary | ios_base::trunc);
//Make sure we could open the stream (this is really the only thing that can go around)
if(!ofs.is_open()) {
cout<<"--------"<<endl;
cout<<"-Error dumping header file.";
cout<<"-Could not open stream to file: '"<<dumpFileName<<"'"<<endl;
cout<<"-The path is probably incorrect or does not exist."<<endl;
return;
}
double NOBOND = -1;
list <Molecule *> molList; list <Molecule *>::iterator molIter;
for(int j=0; j<mt->getMoleculeCount(); j++) {
//First, write out this molecules unique ID
Molecule *m=mt->getMolecule(j);
double uId = (double)m->getUniqueID();
ofs.write((char *)&uId,sizeof(double));
//Second, output the complex number so we can quickly recover
//the complexes
if(!s->isUsingComplex()) {
if(m->getComplexID()==-1) { //if we haven't visited this guy yet...
m->traverseBondedNeighborhood(molList,ReactionClass::NO_LIMIT);
for(molIter=molList.begin(); molIter!=molList.end(); molIter++) {
(*molIter)->setComplexID((int)complexCount);
}
ofs.write((char *)&complexCount,sizeof(double));
complexCount++;
molList.clear();
} else {
double thisUid = m->getComplexID();
ofs.write((char *)&thisUid,sizeof(double));
}
} else {
complexCount = m->getComplexID();
ofs.write((char *)&complexCount,sizeof(double));
}
//Now export all the components, marking its state and
//binding partner if any
for(int k=0; k<mt->getNumOfComponents(); k++) {
double stateValue = (double)m->getComponentState(k);
ofs.write((char *)&stateValue,sizeof(double));
if(!m->isBindingSiteBonded(k)) {
ofs.write((char *)&NOBOND,sizeof(double));
} else {
Molecule *m2=m->getBondedMolecule(k);
double uId2 = (double)m2->getUniqueID();
ofs.write((char *)&uId2,sizeof(double));
}
}
for(int k=0; k<mt->getNumOfTypeIFunctions(); k++) {
double val = m->getLocalFunctionValue(k);
LocalFunction *lf = m->getLocalFunction(k);
double localValue = lf->evaluateOn(m,LocalFunction::MOLECULE);
ofs.write((char *)&val,sizeof(double));
ofs.write((char *)&localValue,sizeof(double));
// ofs<<"\t"<<i<<"\t"<<k<<"\t"<<mt->getTypeIILocalFunction(k)->getName()<<"\n";
}
}
ofs.flush();
ofs.close();
}
}
