Grid¶

class sisl.Grid(shape, bc=None, sc=None, dtype=None, geom=None)[source]¶

Object to retain grid information

This grid object handles cell vectors and divisions of said grid.

A grid can be periodic and non-periodic.

Attributes

`DIRICHLET`
`NEUMANN`
`PERIODIC`
`cell`	Returns the inherent `SuperCell` objects `cell`
`dcell`	Returns the delta-cell
`dtype`	Returns the data-type of the grid
`dvol`	Volume of the grids voxel elements
`isc_off`	Returns the inherent `SuperCell` objects `isc_off`
`n_s`	Returns the inherent `SuperCell` objects `n_s`
`nsc`	Returns the inherent `SuperCell` objects `nsc`
`rcell`	Returns the inherent `SuperCell` objects `rcell`
`sc_off`	Returns the inherent `SuperCell` objects `sc_off`
`shape`	Returns the shape of the grid
`size`	Returns size of the grid
`vol`	Returns the inherent `SuperCell` objects `vol`

Methods

`__init__`(shape[, bc, sc, dtype, geom])	Initialize a `Grid` object.
`add_vacuum`(vacuum, axis)	Add vacuum along the axis lattice vector
`append`(other, axis)	Appends other `Grid` to this grid along axis
`average`(axis)	Returns the average grid along direction axis
`copy`()	Returns a copy of the object.
`cross_section`(idx, axis)	Takes a cross-section of the grid along axis axis
`index`(coord[, axis])	Returns the index along axis axis where coord exists
`interp`(shape[, method])	Returns an interpolated version of the grid
`is_orthogonal`()	Return true if all cell vectors are linearly independent
`mean`(axis)	Returns the average grid along direction axis
`read`(sile, args, *kwargs)	Reads grid from the `Sile` using read_grid
`remove`(idx, axis)	Removes certain indices from a specified axis.
`remove_part`(idx, axis, above)	Removes parts of the grid via above/below designations.
`sc_index`(args, *kwargs)	Call local `SuperCell` object `sc_index` function
`set_bc`([boundary, a, b, c])	Set the boundary conditions on the grid
`set_boundary`([boundary, a, b, c])	Set the boundary conditions on the grid
`set_boundary_condition`([boundary, a, b, c])	Set the boundary conditions on the grid
`set_geom`(geom)	Sets the `Geometry` for the grid.
`set_geometry`(geom)	Sets the `Geometry` for the grid.
`set_grid`(shape[, dtype])	Create the internal grid of certain size.
`set_nsc`(args, *kwargs)	Set the number of super-cells in the `SuperCell` object
`set_sc`(sc)	Overwrites the local supercell
`set_supercell`(sc)	Overwrites the local supercell
`sub`(idx, axis)	Retains certain indices from a specified axis.
`sub_part`(idx, axis, above)	Retains parts of the grid via above/below designations.
`sum`(axis)	Returns the grid summed along axis axis.
`swapaxes`(a, b)	Returns Grid with swapped axis
`write`(sile, args, *kwargs)	Writes grid to the `Sile` using write_grid

DIRICHLET = 3¶

NEUMANN = 2¶

PERIODIC = 1¶

add_vacuum(vacuum, axis)¶

Add vacuum along the axis lattice vector

Parameters:

vacuum : float

amount of vacuum added, in Ang

axis : int

the lattice vector to add vacuum along

append(other, axis)[source]¶: Appends other Grid to this grid along axis

average(axis)[source]¶: Returns the average grid along direction axis

cell¶: Returns the inherent SuperCell objects cell

copy()[source]¶: Returns a copy of the object.

cross_section(idx, axis)[source]¶

Takes a cross-section of the grid along axis axis

Remark: This API entry might change to handle arbitrary cuts via rotation of the axis

dcell¶: Returns the delta-cell

dtype¶: Returns the data-type of the grid

dvol¶: Volume of the grids voxel elements

index(coord, axis=None)[source]¶

Returns the index along axis axis where coord exists

Parameters:

coord : array_like or float

the coordinate of the axis

axis : int

the axis direction of the index

interp(shape, method='linear', **kwargs)[source]¶

Returns an interpolated version of the grid

Parameters:

shape : int, array_like

the new shape of the grid

method : str

the method used to perform the interpolation, see scipy.interpolate.interpn for further details.

**kwargs :

optional arguments passed to the interpolation algorithm The interpolation routine is scipy.interpolate.interpn

is_orthogonal()¶: Return true if all cell vectors are linearly independent

isc_off¶: Returns the inherent SuperCell objects isc_off

mean(axis)¶: Returns the average grid along direction axis

n_s¶: Returns the inherent SuperCell objects n_s

nsc¶: Returns the inherent SuperCell objects nsc

rcell¶: Returns the inherent SuperCell objects rcell

static read(sile, *args, **kwargs)[source]¶

Reads grid from the Sile using read_grid

Parameters:

sile : Sile, str

a Sile object which will be used to read the grid if it is a string it will create a new sile using get_sile.

* : args passed directly to read_grid(,**)

remove(idx, axis)[source]¶

Removes certain indices from a specified axis.

Works exactly opposite to sub.

Parameters:

idx : array_like

the indices of the grid axis axis to be removed

axis : int

the axis segment from which we remove all indices idx

remove_part(idx, axis, above)[source]¶

Removes parts of the grid via above/below designations.

Works exactly opposite to sub_part

Parameters:

idx : array_like

the indices of the grid axis axis to be removed for above=True grid[:idx,...] for above=False grid[idx:,...]

axis : int

the axis segment from which we retain the indices idx

above: bool

if True will retain the grid:

grid[:idx,...]

else it will retain the grid:

grid[idx:,...]

sc_index(*args, **kwargs)¶: Call local SuperCell object sc_index function

sc_off¶: Returns the inherent SuperCell objects sc_off

set_bc(boundary=None, a=None, b=None, c=None)[source]¶

Set the boundary conditions on the grid

Parameters:

boundary: (3, ) or int, optional

boundary condition for all boundaries (or the same for all)

a: int, optional

boundary condition for the first unit-cell vector direction

b: int, optional

boundary condition for the second unit-cell vector direction

c: int, optional

boundary condition for the third unit-cell vector direction

set_boundary(boundary=None, a=None, b=None, c=None)¶

Set the boundary conditions on the grid

Parameters:

boundary: (3, ) or int, optional

boundary condition for all boundaries (or the same for all)

a: int, optional

boundary condition for the first unit-cell vector direction

b: int, optional

boundary condition for the second unit-cell vector direction

c: int, optional

boundary condition for the third unit-cell vector direction

set_boundary_condition(boundary=None, a=None, b=None, c=None)¶

Set the boundary conditions on the grid

Parameters:

boundary: (3, ) or int, optional

boundary condition for all boundaries (or the same for all)

a: int, optional

boundary condition for the first unit-cell vector direction

b: int, optional

boundary condition for the second unit-cell vector direction

c: int, optional

boundary condition for the third unit-cell vector direction

set_geom(geom)¶

Sets the Geometry for the grid.

Setting the Geometry for the grid is a possibility to attach atoms to the grid.

It is not a necessary entity.

set_geometry(geom)[source]¶

Sets the Geometry for the grid.

Setting the Geometry for the grid is a possibility to attach atoms to the grid.

It is not a necessary entity.

set_grid(shape, dtype=None)[source]¶: Create the internal grid of certain size.

set_nsc(*args, **kwargs)¶

Set the number of super-cells in the SuperCell object

See set_nsc for allowed parameters.