AvogadroLibs  1.96.0
Public Types | Static Public Member Functions | List of all members
CrystalTools Class Reference

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

#include <avogadro/core/crystaltools.h>

Public Types

enum  Option {
  None = 0x0 ,
  TransformAtoms = 0x1
}
 The Option enum provides bitwise option flags for the various algorithms. More...
 
typedef int Options
 

Static Public Member Functions

static bool wrapAtomsToUnitCell (Molecule &molecule)
 
static bool rotateToStandardOrientation (Molecule &molecule, Options opts=None)
 
static bool setVolume (Molecule &molecule, Real newVolume, Options opts=None)
 
static bool niggliReduce (Molecule &molecule, Options opts=None)
 
static bool isNiggliReduced (const Molecule &mol)
 
static bool buildSupercell (Molecule &molecule, unsigned int a, unsigned int b, unsigned int c)
 
static bool setCellMatrix (Molecule &molecule, const Matrix3 &newCellColMatrix, Options opt=None)
 
static bool fractionalCoordinates (const UnitCell &unitCell, const Array< Vector3 > &cart, Array< Vector3 > &frac)
 
static bool fractionalCoordinates (const Molecule &molecule, Array< Vector3 > &coords)
 
static bool setFractionalCoordinates (Molecule &molecule, const Array< Vector3 > &coords)
 

Member Enumeration Documentation

◆ Option

enum Option
Enumerator
None 

No options specified.

TransformAtoms 

Transform atoms along with the unit cell.

Member Function Documentation

◆ wrapAtomsToUnitCell()

static bool wrapAtomsToUnitCell ( Molecule molecule)
static

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.

◆ rotateToStandardOrientation()

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

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
optsIf TransformAtoms is specified, the atoms in molecule are rotated along with the unit cell.
Returns
True on success, false otherwise.

◆ setVolume()

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

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

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

◆ niggliReduce()

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

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
optsIf 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.

◆ isNiggliReduced()

static bool isNiggliReduced ( const Molecule mol)
static

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.

◆ buildSupercell()

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

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
aThe number of units along lattice vector a for the supercell
bThe number of units along lattice vector b for the supercell
cThe number of units along lattice vector c for the supercell
Returns
True on success, false on failure.

◆ setCellMatrix()

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

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
optIf 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.

◆ fractionalCoordinates() [1/2]

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

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.

◆ fractionalCoordinates() [2/2]

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

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.

◆ setFractionalCoordinates()

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

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

Returns

The documentation for this class was generated from the following file: