Unit Cell¶

class chemfiles::UnitCell

An UnitCell represent the box containing the atoms, and its periodicity.

A unit cell is fully represented by three lenghts (a, b, c); and three angles (alpha, beta, gamma). The angles are stored in degrees, and the lenghts in Angstroms.

A cell also has a matricial representation, by projecting the three base vector into an orthonormal base. We choose to represent such matrix as an upper triangular matrix:

            | a_x   b_x   c_x |
            |  0    b_y   c_y |
            |  0     0    c_z |

An unit cell also have a cell type, represented by the CellType enum.

Public Functions

UnitCell(const UnitCell & other): Copy constructor.

UnitCell(UnitCell && other): Move constructor.

UnitCell(): Construct an INFINITE unit cell.

UnitCell(double a): Construct a cubic unit cell of side size a

UnitCell(double a, double b, double c): Construct an ORTHOROMBIC unit cell of side size a, b, c

UnitCell(double a, double b, double c, double alpha, double beta, double gamma): Construct a TRICLINIC unit cell of side size a, b, c, and cell angles alpha, beta, gamma

UnitCell(CellType type): Construct a cell of type type, with all lenghts set to 0 and all angles set to 90°

UnitCell(CellType type, double a): Construct a cell of type type, with all lenghts set to a and all angles set to 90°

UnitCell(CellType type, double a, double b, double c): Construct a cell of type type, with lenghts set to a ,b, d, and all angles set to 90°

Matrix3D matricial() const: Get a matricial representation of the cell.

void raw_matricial(double matrix[3][3]) const: Populate C-style matricial representation of the cell. The array should have a 3 x 3 size.

CellType type() const: Get the cell type.

void type(CellType t): Set the cell type to t.

double a() const: Get the first lenght (a) of the cell.

void set_a(double val): Set the first lenght (a) of the cell.

double b() const: Get the second lenght (b) of the cell.

void set_b(double val): Set the second lenght (b) of the cell.

double c() const: Get the third lenght (c) of the cell.

void set_c(double val): Set the third lenght (c) of the cell.

double alpha() const: Get the first angle (alpha) of the cell.

void set_alpha(double val): Set the first angle (alpha) of the cell if possible.

double beta() const: Get the second angle (beta) of the cell.

void set_beta(double val): Set the second angle (beta) of the cell if possible.

double gamma() const: Get the third angle (gamma) of the cell.

void set_gamma(double val): Set the third angle (gamma) of the cell if possible.

double volume() const: Get the unit cell volume.

Vector3D wrap(const Vector3D & vect) const: Wrap the vector vect in the unit cell, using periodic boundary conditions.

CellType enum

Values:

ORTHORHOMBIC = = 0 -
Orthorhombic cell, with the three angles equals to 90°
TRICLINIC = = 1 -
Triclinic cell, with any values for the angles.
INFINITE = = 2 -
Infinite cell, to use when there is no cell.