# `CHFL_CELL`¶

typedef struct CHFL_CELL CHFL_CELL

An opaque type handling an unit cell.

A `CHFL_CELL` represent the box containing the atoms, and its periodicity.

An unit cell is fully represented by three lengths (a, b, c); and three angles (alpha, beta, gamma). The angles are stored in degrees, and the lengths 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 |
```

Here is the full list of functions acting on `CHFL_CELL`:

CHFL_CELL *chfl_cell(const chfl_vector3d lengths, const chfl_vector3d angles)

Create an unit cell using the optional `lengths` and `angles` parameters

If both `lengths` and `angles` are NULL, this creates an infinite unit cell. If `angles` is NULL, it defaults to `[90, 90, 90]`.

The shape of the cell depends on the angles: it will be ORTHORHOMBIC if the three angles are 90°, TRICLINIC otherwise.

The cell lengths should be in Angstroms, and the angles in degree.

The caller of this function should free the associated memory using `chfl_free`.

Returns:

A pointer to the unit cell, or NULL in case of error. You can use `chfl_last_error` to learn about the error.

CHFL_CELL *chfl_cell_from_matrix(const chfl_vector3d matrix[3])

Create an unit cell from the unit cell matrix.

If `matrix` contains only zeros, then an infinite cell is created. If only the diagonal of the matrix is non-zero, then the cell is `ORTHORHOMBIC`. Else a `TRICLINIC` cell is created. The matrix entries should be in Angstroms.

The caller of this function should free the associated memory using `chfl_free`.

Returns:

A pointer to the unit cell, or NULL in case of error. You can use `chfl_last_error` to learn about the error.

CHFL_CELL *chfl_cell_from_frame(CHFL_FRAME *frame)

Get access to the cell of a `frame`

Any modification to the cell will be reflected in the `frame`. The `frame` will be kept alive, even if `chfl_free(frame)` is called, until `chfl_free` is also called on the pointer returned by this function.

If `chfl_frame_set_cell` is called, this pointer will point to the new cell.

Returns:

A pointer to the unit cell, or NULL in case of error. You can use `chfl_last_error` to learn about the error.

CHFL_CELL *chfl_cell_copy(const CHFL_CELL *cell)

Get a copy of a `cell`.

The caller of this function should free the associated memory using `chfl_free`.

Returns:

A pointer to the new cell, or NULL in case of error. You can use `chfl_last_error` to learn about the error.

chfl_status chfl_cell_volume(const CHFL_CELL *cell, double *volume)

Get the unit cell volume of `cell` in the double pointed to by `volume`.

Returns:

The operation status code. You can use `chfl_last_error` to learn about the error if the status code is not `CHFL_SUCCESS`.

chfl_status chfl_cell_lengths(const CHFL_CELL *cell, chfl_vector3d lengths)

Get the unit cell lengths in `lengths`. The cell lengths are in Angstroms.

Returns:

The operation status code. You can use `chfl_last_error` to learn about the error if the status code is not `CHFL_SUCCESS`.

chfl_status chfl_cell_set_lengths(CHFL_CELL *cell, const chfl_vector3d lengths)

Set the unit cell lengths to `lengths`.

The cell lengths should be in Angstroms.

This function reset cell orientation!

After the call, the cell is aligned such that the first cell vector is along the x axis, and the second cell vector is in the xy plane.

Returns:

The operation status code. You can use `chfl_last_error` to learn about the error if the status code is not `CHFL_SUCCESS`.

chfl_status chfl_cell_angles(const CHFL_CELL *cell, chfl_vector3d angles)

Get the cell angles in `angles`. The cell angles are in degrees.

Returns:

The operation status code. You can use `chfl_last_error` to learn about the error if the status code is not `CHFL_SUCCESS`.

chfl_status chfl_cell_set_angles(CHFL_CELL *cell, const chfl_vector3d angles)

Set the cell angles to `angles`.

The cell lengths should be in degree. Trying to set cell angles on a cell which is not triclinic (does not have the `CHFL_CELL_TRICLINIC` shape) is an error.

This function reset cell orientation!

After the call, the cell is aligned such that the first cell vector is along the x axis, and the second cell vector is in the xy plane.

Returns:

The operation status code. You can use `chfl_last_error` to learn about the error if the status code is not `CHFL_SUCCESS`.

chfl_status chfl_cell_matrix(const CHFL_CELL *cell, chfl_vector3d matrix[3])

Get the unit `cell` matricial representation in `matrix`.

Returns:

The operation status code. You can use `chfl_last_error` to learn about the error if the status code is not `CHFL_SUCCESS`.

enum chfl_cellshape

Available cell shapes in chemfiles.

Values:

enumerator CHFL_CELL_ORTHORHOMBIC

The three angles are 90°

enumerator CHFL_CELL_TRICLINIC

The three angles may not be 90°

enumerator CHFL_CELL_INFINITE

Cell shape when there is no periodic boundary conditions.

chfl_status chfl_cell_shape(const CHFL_CELL *cell, chfl_cellshape *shape)

Get the unit `cell` shape in `shape`.

Returns:

The operation status code. You can use `chfl_last_error` to learn about the error if the status code is not `CHFL_SUCCESS`.

chfl_status chfl_cell_set_shape(CHFL_CELL *cell, chfl_cellshape shape)

Set the unit `cell` shape to `shape`.

Returns:

The operation status code. You can use `chfl_last_error` to learn about the error if the status code is not `CHFL_SUCCESS`.

chfl_status chfl_cell_wrap(const CHFL_CELL *cell, chfl_vector3d vector)

Wrap a `vector` in the unit `cell`.

Returns:

The operation status code. You can use `chfl_last_error` to learn about the error if the status code is not `CHFL_SUCCESS`.