sisl.io.cubeSile

class sisl.io.cubeSile(filename, *args, **kwargs)

Bases: Sile

CUBE file object

By default the cube file is written using Bohr units. one can define the units by passing a respective unit argument. Note that the grid data is assumed unit-less and thus no conversion will be done for this data, only atomic coordinates and lattice vectors.

Methods

base_directory([relative_to])

Retrieve the base directory of the file, relative to the path relative_to

close()

dir_file([filename, filename_base])

File of the current Sile

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

read_basis()

Reads the Atoms object from the CUBE file

read_geometry()

Returns Geometry object from the CUBE file

read_grid([imag])

Returns Grid object from the CUBE file

read_lattice([ret_na])

Returns Lattice object from the CUBE file

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

write_geometry(geometry[, fmt, size, ...])

Writes Geometry object attached to this grid

write_grid(grid[, fmt, imag, unit])

Write Grid to the contained file

write_lattice(lattice[, fmt, size, origin, unit])

Writes Lattice object attached to this grid

base_file

File of the current Sile

file

File of the current Sile

plot

Handles all plotting possibilities for a class
__init__(filename, mode='r', *args, **kwargs)

Just to pass away the args and kwargs

base_directory(relative_to='.')

Retrieve the base directory of the file, relative to the path relative_to

property base_file

File of the current Sile

close()
dir_file(filename=None, filename_base='')

File of the current Sile

property file

File of the current Sile

plot

Handles all plotting possibilities for a class

read(*args, **kwargs)

Generic read method which should be overloaded in child-classes

Parameters:

kwargs – keyword arguments will try and search for the attribute read_<> and call it with the remaining **kwargs as arguments.

read_basis() → Atoms[source]

Reads the Atoms object from the CUBE file

Return type:

Atoms

read_geometry() → Geometry[source]

Returns Geometry object from the CUBE file

Return type:

Geometry

read_grid(imag=None) → Grid[source]

Returns Grid object from the CUBE file

Parameters:

imag (str or Sile or Grid) – the imaginary part of the grid. If the geometries does not match an error will be raised.

Return type:

Grid

read_lattice(ret_na: bool = False) → Lattice[source]

Returns Lattice object from the CUBE file

Parameters:

ret_na (bool, optional) – whether to also return the number of atoms in the geometry

Returns:

  • lattice (Lattice) – the lattice object

  • na (int) – number of atoms (only if ret_na)

Return type:

Lattice

write(*args, **kwargs)

Generic write method which should be overloaded in child-classes

Parameters:

**kwargs – keyword arguments will try and search for the attribute write_ and call it with the remaining **kwargs as arguments.

write_geometry(geometry: Geometry, fmt: str = '15.10e', size=None, origin=None, unit: str = 'Bohr', *args, **kwargs)[source]

Writes Geometry object attached to this grid

Parameters:

  • geometry (Geometry) – geometry to be written

  • fmt (str) – floating point format for stored values

  • size ((3, ), optional) – shape of the stored grid ([1, 1, 1])

  • origin ((3, ), optional) – origin of the cell ([0, 0, 0])

  • unit (str) – what length unit should the cube file data be written in

write_grid(grid: Grid, fmt: str = '.5e', imag: bool = False, unit: str = 'Bohr', *args, **kwargs)[source]

Write Grid to the contained file

Parameters:

  • grid (Grid) – the grid to be written in the CUBE file

  • fmt (str) – format used for precision output

  • imag (bool) – write only imaginary part of the grid, default to only writing the real part.

  • unit (str) – what length unit should the cube file data be written in. The grid data is assumed to be unit-less, this unit only refers to the lattice vectors and atomic coordinates.

  • buffersize (int, optional) – size of the buffer while writing the data, (6144)

write_lattice(lattice: Lattice, fmt: str = '15.10e', size=None, origin=None, unit: str = 'Bohr', *args, **kwargs)[source]

Writes Lattice object attached to this grid

Parameters:

  • lattice (Lattice) – lattice to be written

  • fmt (str) – floating point format for stored values

  • size ((3, ), optional) – shape of the stored grid ([1, 1, 1])

  • origin ((3, ), optional) – origin of the cell ([0, 0, 0])

  • unit (str) – what length unit should the cube file data be written in