sisl.io.siesta.gridncSileSiesta
- class sisl.io.siesta.gridncSileSiesta(filename, mode='r', lvl=0, access=1, *args, **kwargs)
Bases:
SileCDFSiesta
NetCDF real-space grid file
The grid sile will automatically convert the units from Siesta units (Bohr, Ry) to sisl units (Ang, eV) provided the correct extension is present.
Plotting
Plotting functions for the
gridncSileSiesta
class.plot.grid
([index, name, ...])Calls
read_grid
and creates aGridPlot
from its output.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
iter
([group, dimension, variable, levels, root])Iterator on all groups, variables and dimensions.
read
(*args, **kwargs)Generic read method which should be overloaded in child-classes
read_grid
([index, name])Reads a grid in the current Siesta.grid.nc file
Returns a Lattice object from a Siesta.grid.nc file
write
(*args, **kwargs)Generic write method which should be overloaded in child-classes
write_grid
(grid[, spin, nspin])Write a grid to the grid.nc file
write_lattice
(lattice)Write a supercell to the grid.nc file
Attributes
File of the current Sile
File of the current Sile
- base_directory(relative_to='.')
Retrieve the base directory of the file, relative to the path relative_to
- close()
- dir_file(filename=None, filename_base='')
File of the current Sile
- iter(group=True, dimension=True, variable=True, levels=-1, root=None)
Iterator on all groups, variables and dimensions.
This iterator iterates through all groups, variables and dimensions in the
Dataset
The generator sequence will _always_ be:
Group
Dimensions in group
Variables in group
As the dimensions are generated before the variables it is possible to copy groups, dimensions, and then variables such that one always ensures correct dependencies in the generation of a new
SileCDF
.- Parameters:
group (
bool
(True)) – whether the iterator yields Group instancesdimension (
bool
(True)) – whether the iterator yields Dimension instancesvariable (
bool
(True)) – whether the iterator yields Variable instanceslevels (
int
(-1)) – number of levels to traverse, with respect toroot
variable, i.e. number of sub-groups this iterator will return.root (
str
(None)) – the base root to start iterating from.
Examples
Script for looping and checking each instance.
>>> for gv in self.iter(): ... if self.isGroup(gv): ... # is group ... elif self.isDimension(gv): ... # is dimension ... elif self.isVariable(gv): ... # is variable
- plot.grid(index=0, name='gridfunc', *args, data_kwargs={}, axes: Axes = ['z'], represent: Literal['real', 'imag', 'mod', 'phase', 'deg_phase', 'rad_phase'] = 'real', transforms: Sequence[str | Callable] = (), reduce_method: Literal['average', 'sum'] = 'average', boundary_mode: str = 'grid-wrap', nsc: tuple[int, int, int] = (1, 1, 1), interp: tuple[int, int, int] = (1, 1, 1), isos: Sequence[dict] = [], smooth: bool = False, colorscale: Colorscale | None = None, crange: tuple[float, float] | None = None, cmid: float | None = None, show_cell: Literal['box', 'axes', False] = 'box', cell_style: dict = {}, x_range: Sequence[float] | None = None, y_range: Sequence[float] | None = None, z_range: Sequence[float] | None = None, plot_geom: bool = False, geom_kwargs: dict = {}, backend: str = 'plotly') GridPlot
Calls
read_grid
and creates aGridPlot
from its output.- Parameters:
index (
int
orarray_like
, optional) – the spin-index for retrieving one of the components. If a vector is passed it refers to the fraction per indexed component. I.e.[0.5, 0.5]
will return sum of half the first two components. Default to the first component.name (
str
, optional) – the name for the grid-function (do not supply for standard Siesta output)geometry (
Geometry
, optional) – add the Geometry to the Gridspin (optional) – same as index argument. spin argument has precedence.
axes – The axes to project the grid to.
represent – The representation of the grid to plot.
transforms – List of transforms to apply to the grid before plotting.
reduce_method – The method used to reduce the grid axes that are not displayed.
boundary_mode – The method used to deal with the boundary conditions. Only used if the grid is to be orthogonalized. See scipy docs for more info on the possible values.
nsc – The number of unit cells to display in each direction.
interp – The interpolation factor to use for each axis to make the grid smoother.
isos – List of isosurfaces or isocontours to plot. See the showcase notebooks for examples.
smooth – Whether to ask the plotting backend to make an attempt at smoothing the grid display.
colorscale – Colorscale to use for the grid display in the 2D representation. If None, the default colorscale is used for each backend.
crange – Min and max values for the colorscale.
cmid – The value at which the colorscale is centered.
show_cell – Method used to display the unit cell. If False, the cell is not displayed.
cell_style – Style specification for the cell. See the showcase notebooks for examples.
x_range – The range of the x axis to take into account. Even if the X axis is not displayed! This is important because the reducing operation will only be applied on this range.
y_range – The range of the y axis to take into account. Even if the Y axis is not displayed! This is important because the reducing operation will only be applied on this range.
z_range – The range of the z axis to take into account. Even if the Z axis is not displayed! This is important because the reducing operation will only be applied on this range.
plot_geom – Whether to plot the associated geometry (if any).
geom_kwargs – Keyword arguments to pass to the geometry plot of the associated geometry.
backend – The backend to use to generate the figure.
See also
GridPlot
The plot class used to generate the plot.
read_grid
The method called to get the data.
- 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_grid(index=0, name='gridfunc', *args, **kwargs) Grid [source]
Reads a grid in the current Siesta.grid.nc file
Enables the reading and processing of the grids created by Siesta
- Parameters:
index (
int
orarray_like
, optional) – the spin-index for retrieving one of the components. If a vector is passed it refers to the fraction per indexed component. I.e.[0.5, 0.5]
will return sum of half the first two components. Default to the first component.name (
str
, optional) – the name for the grid-function (do not supply for standard Siesta output)geometry (
Geometry
, optional) – add the Geometry to the Gridspin (optional) – same as index argument. spin argument has precedence.
- 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.
- property base_file
File of the current Sile
- property file
File of the current Sile
- plot
Plotting functions for the
gridncSileSiesta
class.