void
CFactorGraph::createGroups (void)
{
VarSignMap varGroups;
FacSignMap facGroups;
unsigned nIters = 0;
bool groupsHaveChanged = true;
const VarNodes& varNodes = groundFg_->varNodes();
const FacNodes& facNodes = groundFg_->facNodes();
while (groupsHaveChanged || nIters == 1) {
nIters ++;
unsigned prevFactorGroupsSize = facGroups.size();
facGroups.clear();
// set a new color to the factors with the same signature
for (unsigned i = 0; i < facNodes.size(); i++) {
const Signature& signature = getSignature (facNodes[i]);
FacSignMap::iterator it = facGroups.find (signature);
if (it == facGroups.end()) {
it = facGroups.insert (make_pair (signature, FacNodes())).first;
}
it->second.push_back (facNodes[i]);
}
for (FacSignMap::iterator it = facGroups.begin();
it != facGroups.end(); it++) {
Color newColor = getFreeColor();
FacNodes& groupMembers = it->second;
for (unsigned i = 0; i < groupMembers.size(); i++) {
setColor (groupMembers[i], newColor);
}
}
// set a new color to the variables with the same signature
unsigned prevVarGroupsSize = varGroups.size();
varGroups.clear();
for (unsigned i = 0; i < varNodes.size(); i++) {
const Signature& signature = getSignature (varNodes[i]);
VarSignMap::iterator it = varGroups.find (signature);
if (it == varGroups.end()) {
it = varGroups.insert (make_pair (signature, VarNodes())).first;
}
it->second.push_back (varNodes[i]);
}
for (VarSignMap::iterator it = varGroups.begin();
it != varGroups.end(); it++) {
Color newColor = getFreeColor();
VarNodes& groupMembers = it->second;
for (unsigned i = 0; i < groupMembers.size(); i++) {
setColor (groupMembers[i], newColor);
}
}
groupsHaveChanged = prevVarGroupsSize != varGroups.size()
|| prevFactorGroupsSize != facGroups.size();
}
printGroups (varGroups, facGroups);
createClusters (varGroups, facGroups);
}
//! @brief read the actual phase space information
unsigned long OneCLJGenerator::readPhaseSpace(ParticleContainer* particleContainer, std::list<ChemicalPotential>* lmu,
Domain* domain, DomainDecompBase* domainDecomp) {
vector<double> bBoxMin;
vector<double> bBoxMax;
// This is rather a hack to make sure that the ids of the molecules for each process are unique
_moleculeCountOffset = (2 * domainDecomp->getRank()) * _numberOfMolecules / domainDecomp->getNumProcs();
Log::global_log->info() << "MoleculeCountOffset=" << _moleculeCountOffset << endl;
bBoxMin.resize(3);
bBoxMax.resize(3);
for (int i = 0; i < 3; i++) {
bBoxMin[i] = domainDecomp->getBoundingBoxMin(i, domain);
bBoxMax[i] = domainDecomp->getBoundingBoxMax(i, domain);
}
if (_mode == "Homogeneous") {
Log::global_log->info() << "OneCLJGenerator generating molecules. mode: " << _mode << " rho " << _rho << " T "
<< _temperature << " #molecules " << _numberOfMolecules << endl;
createHomogeneousDist(particleContainer, bBoxMin, bBoxMax, domain, domainDecomp);
} else if (_mode == "Cluster") {
Log::global_log->info() << "OneCLJGenerator generating cluster distribution. " << " T " << _temperature
<< " #molecules " << _numberOfMolecules << " rho_gas " << _gasDensity << " rho_fluid " << _fluidDensity
<< endl;
createClusters(particleContainer, bBoxMin, bBoxMax, domain, domainDecomp);
} else {
Log::global_log->error() << "Unknown mode \"" << _mode << "\"!" << endl;
exit(1);
}
vector<Component>& dcomponents = domain->getComponents();
vector<unsigned long> partsPerComp;
partsPerComp.resize(1);
particleContainer->update();
particleContainer->deleteOuterParticles();
domain->setglobalNumMolecules(domainDecomp->countMolecules(particleContainer, partsPerComp));
for (unsigned int i = 0; i < partsPerComp.size(); i++) {
dcomponents[i].setNumMolecules(partsPerComp[i]);
domain->setglobalRotDOF(partsPerComp[i] * dcomponents[i].getRotationalDegreesOfFreedom());
}
domain->setglobalRho(domain->getglobalNumMolecules() / (_simBoxLength[0] * _simBoxLength[1] * _simBoxLength[2]));
return domain->getglobalNumMolecules();
}
int main(int argv, char *argc[])
{
int return_value;
numAlignsInCluster=0;
FILE *fp1, *fp2, *fp3;
fp1=fopen(argc[1],"r");
fp2=fopen(argc[2],"r");
fp3=fopen(argc[3],"w");
maxSizeInst = 330;
if (argv == 5) maxSizeInst=atoi(argc[4]);
//fprintf(stdout, "max Insert size = %d\n", maxSizeInst);
EndClusterR=0;
EndClusterF=0;
return_value = fscanf( fp1,"%s\t%i\n", chroName, &chroSize);
if( return_value != 2)
{
perror( "Error on fscanf");
exit( 1);
}
listOfOEA=(aligns **) malloc(chroSize*sizeof(aligns*));
listOfOEA_R=(int *) malloc(chroSize*sizeof(int));
listOfOEA_F=(int *) malloc(chroSize*sizeof(int));
for (int count=0; count< chroSize; count++)
{
listOfOEA[count]=NULL;
listOfOEA_R[count]=0;
listOfOEA_F[count]=0;
}
// printf("%s\t%i\n", chroName, chroSize);
readTheAligns(fp2);
createClusters(fp3);
}
