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
Reads the
Atoms
object from the CUBE fileReturns
Geometry
object from the CUBE fileread_grid
([imag])Returns Grid object from the CUBE file
read_lattice
([ret_na])Returns
Lattice
object from the CUBE filewrite
(*args, **kwargs)Generic write method which should be overloaded in child-classes
write_geometry
(geometry[, fmt, size, ...])Writes
Geometry
object attached to this gridwrite_grid
(grid[, fmt, imag, unit])Write Grid to the contained file
write_lattice
(lattice[, fmt, size, origin, unit])Writes
Lattice
object attached to this gridFile of the current
Sile
File of the current
Sile
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
- close()
- 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.
- 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
- 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)