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 | ```

Public Types

enum CellShape¶

Possible shapes for the unit cell.

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.

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(CellShape shape)¶

Construct a cell of type `type`, with all lenghts set to 0 and all angles set to 90°

UnitCell(CellShape shape, double a)¶

Construct a cell of type `type`, with all lenghts set to `a` and all angles set to 90°

UnitCell(CellShape shape, 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.

CellShape shape() const¶

Get the cell shape.

void shape(CellShape shape)¶

Set the cell shape to `shape`.

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.