void Foam::pamgPolicy::calcChild()
{
// Algorithm:
// 1) Create temporary equation addressing using a double-pass algorithm.
// to create the offset table.
// 2) Loop through all equations and for each equation find the best fit
// neighbour. If all neighbours are grouped, add equation to best group
// Get addressing
const label nEqns = matrix_.lduAddr().size();
const unallocLabelList& upperAddr = matrix_.lduAddr().upperAddr();
const unallocLabelList& lowerAddr = matrix_.lduAddr().lowerAddr();
// Get off-diagonal matrix coefficients
const scalarField& upper = matrix_.upper();
// For each equation calculate coeffs
labelList cols(upperAddr.size() + lowerAddr.size());
labelList rowOffsets(nEqns + 1);
// Memory management
{
labelList nNbrs(nEqns, 0);
forAll (upperAddr, coeffI)
{
nNbrs[upperAddr[coeffI]]++;
}
forAll (lowerAddr, coeffI)
{
nNbrs[lowerAddr[coeffI]]++;
}
rowOffsets[0] = 0;
forAll (nNbrs, eqnI)
{
rowOffsets[eqnI + 1] = rowOffsets[eqnI] + nNbrs[eqnI];
}
// Reset the list to use as counter
nNbrs = 0;
forAll (upperAddr, coeffI)
{
cols
[
rowOffsets[upperAddr[coeffI]] + nNbrs[upperAddr[coeffI]]
] = coeffI;
nNbrs[upperAddr[coeffI]]++;
}
Foam::tmp<Foam::labelField> Foam::pairGAMGAgglomeration::agglomerate
(
label& nCoarseCells,
const lduAddressing& fineMatrixAddressing,
const scalarField& faceWeights
)
{
const label nFineCells = fineMatrixAddressing.size();
const labelUList& upperAddr = fineMatrixAddressing.upperAddr();
const labelUList& lowerAddr = fineMatrixAddressing.lowerAddr();
// For each cell calculate faces
labelList cellFaces(upperAddr.size() + lowerAddr.size());
labelList cellFaceOffsets(nFineCells + 1);
// memory management
{
labelList nNbrs(nFineCells, 0);
forAll(upperAddr, facei)
{
nNbrs[upperAddr[facei]]++;
}
forAll(lowerAddr, facei)
{
nNbrs[lowerAddr[facei]]++;
}
cellFaceOffsets[0] = 0;
forAll(nNbrs, celli)
{
cellFaceOffsets[celli+1] = cellFaceOffsets[celli] + nNbrs[celli];
}
// reset the whole list to use as counter
nNbrs = 0;
forAll(upperAddr, facei)
{
cellFaces
[
cellFaceOffsets[upperAddr[facei]] + nNbrs[upperAddr[facei]]
] = facei;
nNbrs[upperAddr[facei]]++;
}
void Foam::MGridGenGAMGAgglomeration::
makeCompactCellFaceAddressingAndFaceWeights
(
const lduAddressing& fineAddressing,
List<idxtype>& cellCells,
List<idxtype>& cellCellOffsets,
const scalarField& magSi,
List<scalar>& faceWeights
)
{
const label nFineCells = fineAddressing.size();
const label nFineFaces = fineAddressing.upperAddr().size();
const labelUList& upperAddr = fineAddressing.upperAddr();
const labelUList& lowerAddr = fineAddressing.lowerAddr();
// Number of neighbours for each cell
labelList nNbrs(nFineCells, 0);
forAll(upperAddr, facei)
{
nNbrs[upperAddr[facei]]++;
}
forAll(lowerAddr, facei)
{
nNbrs[lowerAddr[facei]]++;
}
// Set the sizes of the addressing and faceWeights arrays
cellCellOffsets.setSize(nFineCells + 1);
cellCells.setSize(2*nFineFaces);
faceWeights.setSize(2*nFineFaces);
cellCellOffsets[0] = 0;
forAll(nNbrs, celli)
{
cellCellOffsets[celli+1] = cellCellOffsets[celli] + nNbrs[celli];
}
Foam::labelListList Foam::GAMGProcAgglomeration::globalCellCells
(
const lduMesh& mesh
)
{
const lduAddressing& addr = mesh.lduAddr();
lduInterfacePtrsList interfaces = mesh.interfaces();
const label myProcID = Pstream::myProcNo(mesh.comm());
globalIndex globalNumbering
(
addr.size(),
Pstream::msgType(),
mesh.comm(),
Pstream::parRun()
);
labelList globalIndices
(
identity
(
globalNumbering.localSize(myProcID),
globalNumbering.localStart(myProcID)
)
);
// Get the interface cells
PtrList<labelList> nbrGlobalCells(interfaces.size());
{
// Initialise transfer of restrict addressing on the interface
forAll(interfaces, inti)
{
if (interfaces.set(inti))
{
interfaces[inti].initInternalFieldTransfer
(
Pstream::commsTypes::nonBlocking,
globalIndices
);
}
}
if (Pstream::parRun())
{
Pstream::waitRequests();
}
forAll(interfaces, inti)
{
if (interfaces.set(inti))
{
nbrGlobalCells.set
(
inti,
new labelList
(
interfaces[inti].internalFieldTransfer
(
Pstream::commsTypes::nonBlocking,
globalIndices
)
)
);
}
}
}
// Scan the neighbour list to find out how many times the cell
// appears as a neighbour of the face. Done this way to avoid guessing
// and resizing list
labelList nNbrs(addr.size(), 1);
const labelUList& nbr = addr.upperAddr();
const labelUList& own = addr.lowerAddr();
{
forAll(nbr, facei)
{
nNbrs[nbr[facei]]++;
nNbrs[own[facei]]++;
}
forAll(interfaces, inti)
{
if (interfaces.set(inti))
{
const labelUList& faceCells = interfaces[inti].faceCells();
forAll(faceCells, i)
{
nNbrs[faceCells[i]]++;
}
}
}
}
double getTPSAAtomContribs(const ROMol &mol, std::vector<double> &Vi,
bool force) {
TEST_ASSERT(Vi.size() >= mol.getNumAtoms());
double res = 0;
if (!force && mol.hasProp(common_properties::_tpsaAtomContribs)) {
mol.getProp(common_properties::_tpsaAtomContribs, Vi);
mol.getProp(common_properties::_tpsa, res);
return res;
}
unsigned int nAtoms = mol.getNumAtoms();
std::vector<int> nNbrs(nAtoms, 0), nSing(nAtoms, 0), nDoub(nAtoms, 0),
nTrip(nAtoms, 0), nArom(nAtoms, 0), nHs(nAtoms, 0);
for (ROMol::ConstBondIterator bIt = mol.beginBonds(); bIt != mol.endBonds();
++bIt) {
const Bond *bnd = (*bIt);
if (bnd->getBeginAtom()->getAtomicNum() == 1) {
nNbrs[bnd->getEndAtomIdx()] -= 1;
nHs[bnd->getEndAtomIdx()] += 1;
} else if (bnd->getEndAtom()->getAtomicNum() == 1) {
nNbrs[bnd->getBeginAtomIdx()] -= 1;
nHs[bnd->getBeginAtomIdx()] += 1;
} else if (bnd->getIsAromatic()) {
nArom[bnd->getBeginAtomIdx()] += 1;
nArom[bnd->getEndAtomIdx()] += 1;
} else {
switch (bnd->getBondType()) {
case Bond::SINGLE:
nSing[bnd->getBeginAtomIdx()] += 1;
nSing[bnd->getEndAtomIdx()] += 1;
break;
case Bond::DOUBLE:
nDoub[bnd->getBeginAtomIdx()] += 1;
nDoub[bnd->getEndAtomIdx()] += 1;
break;
case Bond::TRIPLE:
nTrip[bnd->getBeginAtomIdx()] += 1;
nTrip[bnd->getEndAtomIdx()] += 1;
break;
default:
break;
}
}
}
for (unsigned int i = 0; i < nAtoms; ++i) {
const Atom *atom = mol.getAtomWithIdx(i);
int atNum = atom->getAtomicNum();
if (atNum != 7 && atNum != 8) continue;
nHs[i] += atom->getTotalNumHs();
int chg = atom->getFormalCharge();
bool in3Ring = mol.getRingInfo()->isAtomInRingOfSize(i, 3);
nNbrs[i] += atom->getDegree();
double tmp = -1;
if (atNum == 7) {
switch (nNbrs[i]) {
case 1:
if (nHs[i] == 0 && chg == 0 && nTrip[i] == 1)
tmp = 23.79;
else if (nHs[i] == 1 && chg == 0 && nDoub[i] == 1)
tmp = 23.85;
else if (nHs[i] == 2 && chg == 0 && nSing[i] == 1)
tmp = 26.02;
else if (nHs[i] == 2 && chg == 1 && nDoub[i] == 1)
tmp = 25.59;
else if (nHs[i] == 3 && chg == 1 && nSing[i] == 1)
tmp = 27.64;
break;
case 2:
if (nHs[i] == 0 && chg == 0 && nSing[i] == 1 && nDoub[i] == 1)
tmp = 12.36;
else if (nHs[i] == 0 && chg == 0 && nTrip[i] == 1 && nDoub[i] == 1)
tmp = 13.60;
else if (nHs[i] == 1 && chg == 0 && nSing[i] == 2 && in3Ring)
tmp = 21.94;
else if (nHs[i] == 1 && chg == 0 && nSing[i] == 2 && !in3Ring)
tmp = 12.03;
else if (nHs[i] == 0 && chg == 1 && nTrip[i] == 1 && nSing[i] == 1)
tmp = 4.36;
else if (nHs[i] == 1 && chg == 1 && nDoub[i] == 1 && nSing[i] == 1)
tmp = 13.97;
else if (nHs[i] == 2 && chg == 1 && nSing[i] == 2)
tmp = 16.61;
else if (nHs[i] == 0 && chg == 0 && nArom[i] == 2)
tmp = 12.89;
else if (nHs[i] == 1 && chg == 0 && nArom[i] == 2)
tmp = 15.79;
else if (nHs[i] == 1 && chg == 1 && nArom[i] == 2)
tmp = 14.14;
break;
case 3:
if (nHs[i] == 0 && chg == 0 && nSing[i] == 3 && in3Ring)
tmp = 3.01;
else if (nHs[i] == 0 && chg == 0 && nSing[i] == 3 && !in3Ring)
tmp = 3.24;
else if (nHs[i] == 0 && chg == 0 && nSing[i] == 1 && nDoub[i] == 2)
tmp = 11.68;
else if (nHs[i] == 0 && chg == 1 && nSing[i] == 2 && nDoub[i] == 1)
tmp = 3.01;
else if (nHs[i] == 1 && chg == 1 && nSing[i] == 3)
tmp = 4.44;
else if (nHs[i] == 0 && chg == 0 && nArom[i] == 3)
tmp = 4.41;
else if (nHs[i] == 0 && chg == 0 && nSing[i] == 1 && nArom[i] == 2)
tmp = 4.93;
else if (nHs[i] == 0 && chg == 0 && nDoub[i] == 1 && nArom[i] == 2)
tmp = 8.39;
else if (nHs[i] == 0 && chg == 1 && nArom[i] == 3)
tmp = 4.10;
else if (nHs[i] == 0 && chg == 1 && nSing[i] == 1 && nArom[i] == 2)
tmp = 3.88;
break;
case 4:
if (nHs[i] == 0 && nSing[i] == 4 && chg == 1) tmp = 0.0;
break;
}
if (tmp < 0.0) {
tmp = 30.5 - nNbrs[i] * 8.2 + nHs[i] * 1.5;
if (tmp < 0) tmp = 0.0;
}
} else if (atNum == 8) {
switch (nNbrs[i]) {
case 1:
if (nHs[i] == 0 && chg == 0 && nDoub[i] == 1)
tmp = 17.07;
else if (nHs[i] == 1 && chg == 0 && nSing[i] == 1)
tmp = 20.23;
else if (nHs[i] == 0 && chg == -1 && nSing[i] == 1)
tmp = 23.06;
break;
case 2:
if (nHs[i] == 0 && chg == 0 && nSing[i] == 2 && in3Ring)
tmp = 12.53;
else if (nHs[i] == 0 && chg == 0 && nSing[i] == 2 && !in3Ring)
tmp = 9.23;
else if (nHs[i] == 0 && chg == 0 && nArom[i] == 2)
tmp = 13.14;
break;
}
if (tmp < 0.0) {
tmp = 28.5 - nNbrs[i] * 8.6 + nHs[i] * 1.5;
if (tmp < 0) tmp = 0.0;
}
}
Vi[i] = tmp;
res += tmp;
}
mol.setProp(common_properties::_tpsaAtomContribs, Vi, true);
mol.setProp(common_properties::_tpsa, res, true);
return res;
}
