Class Avogadro::Core::CrystalTools#

class CrystalTools#

The CrystalTools class contains a collection of static functions that perform common crystallographic operations on a Core::Molecule.

Public Types

enum Option#

The Option enum provides bitwise option flags for the various algorithms.

Values:

enumerator None#: No options specified.

enumerator TransformAtoms#: Transform atoms along with the unit cell.

typedef int Options#

Public Static Functions

static bool wrapAtomsToUnitCell(Molecule &molecule)#

Adjust the atomic positions in molecule so that the fractional (lattice) coordinates of all atoms are in the range [0, 1].

Returns:: True on success, false otherwise.

static bool rotateToStandardOrientation(Molecule &molecule, Options opts = None)#

This function will rotate the input molecule so that the unit cell’s ‘a’ vector is aligned to the x-axis, and the ‘b’ axis is in the xy-plane. It does not use trig functions or the cell parameters, since such implementations are fragile and cannot handle negative cell angles. The derivation of this algorithm can be found at http://xtalopt.openmolecules.net/misc/rotateToStdOrientation.pdf.

Parameters:: opts – If TransformAtoms is specified, the atoms in molecule are rotated along with the unit cell.
Returns:: True on success, false otherwise.

static bool setVolume(Molecule &molecule, Real newVolume, Options opts = None)#

Isotropically scale the volume of the unit cell in molecule to newVolume (in cubic angstrom).

Parameters:: opts – If TransformAtoms is specified, the atoms in molecule are adjusted so that their fractional (lattice) coordinates are preserved.
Returns:: True on success, false on failure.

static bool niggliReduce(Molecule &molecule, Options opts = None)#

Perform a Niggli reduction on molecule’s unit cell. This produces a canonical unit cell representation that strives to be as cubic as possible.

Note

Implements the niggli reduction algorithm detailed in: Grosse-Kunstleve RW, Sauter NK, Adams PD. Numerically stable algorithms for the computation of reduced unit cells. Acta Crystallographica Section A Foundations of Crystallography. 2003;60(1):1-6.

Parameters:: opts – If TransformAtoms is specified, the atom positions are modified to ensure that the same extended atomic structure from the input is represented by the output.
Returns:: True on success, false on failure.

static bool isNiggliReduced(const Molecule &mol)#: Return true if the unit cell in molecule is already Niggli-reduced. This method checks the conditions listed in the paper Gruber B.. Acta Cryst. A. 1973;29(4):433-440.

static bool buildSupercell(Molecule &molecule, unsigned int a, unsigned int b, unsigned int c)#

Build a supercell by expanding upon the unit cell of molecule. It will only return false if the molecule does not have a unit cell or if a, b, or c is set to zero.

Parameters:

a – The number of units along lattice vector a for the supercell
b – The number of units along lattice vector b for the supercell
c – The number of units along lattice vector c for the supercell

Returns:

True on success, false on failure.

static bool setCellMatrix(Molecule &molecule, const Matrix3 &newCellColMatrix, Options opt = None)#

Set the unit cell in molecule to represent the real-space column-vector unit cell description in newCellColMatrix. A unit cell is created if needed.

Parameters:: opt – If TransformAtoms is specified, the atoms in molecule are adjusted so that their fractional (lattice) coordinates are preserved. This option is ignored if the input molecule has no unit cell.
Returns:: True on success, false otherwise.

static bool fractionalCoordinates(const UnitCell &unitCell, const Array<Vector3> &cart, Array<Vector3> &frac)#

Populate the frac vector with the fractional representation of the cartesian coordinates in cart, using unitCell to perform the coordinate transformation.

Returns:: True on success, false otherwise.

static bool fractionalCoordinates(const Molecule &molecule, Array<Vector3> &coords)#

Populate the coords vector with the fractional coordinates of the atoms in molecule, using the unit cell of molecule to perform the coordinate transformation. Coordinates are ordered the same as the Molecule::atomPositions3d() result.

Returns:: True on success, false otherwise.

static bool setFractionalCoordinates(Molecule &molecule, const Array<Vector3> &coords)#

Set the atomic positions of molecule to the fractional coordinates in coords, using the unit cell of molecule to perform the coordinate transformation.

Returns: