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Copy bonds and bond orders when generating super cells #1898

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Dec 28, 2024
Merged

Copy bonds and bond orders when generating super cells #1898

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43704a8
Copy bonds and bond orders when generating super cells
ghutchis Dec 28, 2024
27a5e17
When filling the unit cell, don't wrap existing atoms
ghutchis Dec 28, 2024
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29 changes: 22 additions & 7 deletions avogadro/core/crystaltools.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -22,7 +22,7 @@ struct WrapAtomsToCellFunctor

void operator()(Vector3& pos) { unitCell.wrapCartesian(pos, pos); }
};
}
} // namespace

bool CrystalTools::wrapAtomsToUnitCell(Molecule& molecule)
{
Expand Down Expand Up @@ -182,7 +182,7 @@ T niggliRound(T v, T dec)
const T shifted = v * shift;
return std::floor(shifted + 0.5) / shift;
}
}
} // namespace

bool CrystalTools::niggliReduce(Molecule& molecule, Options opts)
{
Expand Down Expand Up @@ -433,7 +433,7 @@ bool CrystalTools::niggliReduce(Molecule& molecule, Options opts)

// fix coordinates with COB matrix:
const Matrix3 invCob(cob.inverse());
for (auto & fcoord : fcoords) {
for (auto& fcoord : fcoords) {
fcoord = invCob * fcoord;
}

Expand Down Expand Up @@ -558,6 +558,10 @@ bool CrystalTools::buildSupercell(Molecule& molecule, unsigned int a,
Vector3 newB = oldB * b;
Vector3 newC = oldC * c;

// archive the old bond pairs and orders
Array<std::pair<Index, Index>> bondPairs = molecule.bondPairs();
Array<unsigned char> bondOrders = molecule.bondOrders();

// Add in the atoms to the new subcells of the supercell
Index numAtoms = molecule.atomCount();
Array<Vector3> atoms = molecule.atomPositions3d();
Expand All @@ -578,6 +582,17 @@ bool CrystalTools::buildSupercell(Molecule& molecule, unsigned int a,
}
}

// now we need to add the bonds
unsigned copies = molecule.atomCount() / numAtoms;
// we loop through the original bonds to add copies
for (Index i = 0; i < bondPairs.size(); ++i) {
std::pair<Index, Index> bond = bondPairs.at(i);
for (unsigned j = 0; j < copies; ++j) {
molecule.addBond(bond.first + j * numAtoms, bond.second + j * numAtoms,
bondOrders.at(i));
}
}

// Now set the unit cell
molecule.unitCell()->setAVector(newA);
molecule.unitCell()->setBVector(newB);
Expand All @@ -595,7 +610,7 @@ struct TransformAtomsFunctor

void operator()(Vector3& pos) { pos = transform * pos; }
};
}
} // namespace

bool CrystalTools::setCellMatrix(Molecule& molecule,
const Matrix3& newCellColMatrix, Options opt)
Expand Down Expand Up @@ -625,7 +640,7 @@ struct FractionalCoordinatesFunctor

void operator()(Vector3& pos) { unitCell.toFractional(pos, pos); }
};
}
} // namespace

bool CrystalTools::fractionalCoordinates(const UnitCell& unitCell,
const Array<Vector3>& cart,
Expand Down Expand Up @@ -664,7 +679,7 @@ struct SetFractionalCoordinatesFunctor

Vector3 operator()(const Vector3& pos) { return unitCell.toCartesian(pos); }
};
}
} // namespace

bool CrystalTools::setFractionalCoordinates(Molecule& molecule,
const Array<Vector3>& coords)
Expand All @@ -684,4 +699,4 @@ bool CrystalTools::setFractionalCoordinates(Molecule& molecule,
return true;
}

} // namespace Avogadro
} // namespace Avogadro::Core
9 changes: 6 additions & 3 deletions avogadro/core/spacegroups.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ namespace Avogadro::Core {

unsigned short SpaceGroups::hallNumber(const std::string& spaceGroup)
{
unsigned short hall = 0; // can't find anything
unsigned short hall = 0; // can't find anything
const unsigned short hall_count = 531; // 530 but first one is empty
// some files use " instead of = for the space group symbol
std::string sg = spaceGroup;
Expand Down Expand Up @@ -275,6 +275,9 @@ void SpaceGroups::fillUnitCell(Molecule& mol, unsigned short hallNumber,
for (Index j = 1; j < newAtoms.size(); ++j) {
// The new atoms are in fractional coordinates. Convert to cartesian.
Vector3 newCandidate = uc->toCartesian(newAtoms[j]);
// if we are wrapping to the cell, we need to wrap the new atom
if (wrapToCell)
newCandidate = uc->wrapCartesian(newCandidate);

// If there is already an atom in this location within a
// certain tolerance, do not add the atom.
Expand All @@ -298,8 +301,8 @@ void SpaceGroups::fillUnitCell(Molecule& mol, unsigned short hallNumber,
}
}

if (wrapToCell)
CrystalTools::wrapAtomsToUnitCell(mol);
// if (wrapToCell)
// CrystalTools::wrapAtomsToUnitCell(mol);

// Now we need to generate any copies on the unit boundary
// We need to loop through all the atoms again
Expand Down
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