sisl.grid module¶

Define a grid

This grid is the basis of different used models.

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

Bases: sisl.supercell.SuperCellChild

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

`cell`	Returns the inherent `SuperCell` objects `cell`
`dcell`	Returns the delta-cell
`dtype`	Returns the data-type of the grid
`dvol`	Returns the delta-volume
`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

`ArgumentParser`([parser])	Create and return a group of argument parsers which manipulates it self `Grid`.
`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, args, *kwargs)	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_grid`(shape[, dtype])	Create the internal grid of certain size.
`set_nsc`(nsc)	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)	Writes grid to the `Sile` using `write_grid`

Initialize a Grid object.

Parameters:

shape : list of ints

the size of each grid dimension

bc : int

the boundary condition (Grid.Periodic/Grid.Neumann/Grid.Dirichlet)

sc : SuperCell/list

the associated supercell (

Attributes

`cell`	Returns the inherent `SuperCell` objects `cell`
`dcell`	Returns the delta-cell
`dtype`	Returns the data-type of the grid
`dvol`	Returns the delta-volume
`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

`ArgumentParser`([parser])	Create and return a group of argument parsers which manipulates it self `Grid`.
`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, args, *kwargs)	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_grid`(shape[, dtype])	Create the internal grid of certain size.
`set_nsc`(nsc)	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)	Writes grid to the `Sile` using `write_grid`

ArgumentParser(parser=None, *args, **kwargs)[source]¶

Create and return a group of argument parsers which manipulates it self Grid.

Parameters:

parser: ArgumentParser, None

in case the arguments should be added to a specific parser. It defaults to create a new.

limit_arguments: bool, True

If False additional options will be created which are similar to other options. For instance --repeat-x which is equivalent to --repeat x.

short: bool, False

Create short options for a selected range of options

positional_out: bool, False

If True, adds a positional argument which acts as –out. This may be handy if only the geometry is in the argument list.

Dirichlet = 3¶

Neumann = 2¶

Periodic = 1¶

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

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

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¶: Returns the delta-volume

index(coord, axis=None)[source]¶

Returns the index along axis axis where coord exists

Parameters:

coord : array_like / float

the coordinate of the axis

axis : int

the axis direction of the index

interp(shape, *args, **kwargs)[source]¶

Returns an interpolated version of the grid

Parameters:

shape : int, array_like

the new shape of the grid

*args, **kwargs :

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

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

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:,...]

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

Set the boundary conditions on the grid boundary: [3], integer, optional

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

a: integer, optional: boundary condition for the first unit-cell vector direction
b: integer, optional: boundary condition for the second unit-cell vector direction
c: integer, 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 boundary: [3], integer, optional

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

a: integer, optional: boundary condition for the first unit-cell vector direction
b: integer, optional: boundary condition for the second unit-cell vector direction
c: integer, 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 boundary: [3], integer, optional

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

a: integer, optional: boundary condition for the first unit-cell vector direction
b: integer, optional: boundary condition for the second unit-cell vector direction
c: integer, optional: boundary condition for the third unit-cell vector direction

set_geom(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.

shape¶: Returns the shape of the grid

size¶: Returns size of the grid

sub(idx, axis)[source]¶

Retains certain indices from a specified axis.

Works exactly opposite to remove.

Parameters:

idx : array_like

the indices of the grid axis axis to be retained

axis : int

the axis segment from which we retain the indices idx

sub_part(idx, axis, above)[source]¶

Retains parts of the grid via above/below designations.

Works exactly opposite to remove_part

Parameters:

idx : array_like

the indices of the grid axis axis to be retained 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,...]

sum(axis)[source]¶: Returns the grid summed along axis axis.

swapaxes(a, b)[source]¶

Returns Grid with swapped axis

If swapaxes(0,1) it returns the 0 in the 1 values.

write(sile)[source]¶

Writes grid to the Sile using write_grid

Parameters:

sile : Sile, str

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

sisl.grid.sgrid(grid=None, argv=None, ret_grid=False)[source]¶

Main script for sgrid script.

This routine may be called with argv and/or a Sile which is the grid at hand.

Parameters:

grid : Grid/BaseSile

this may either be the grid, as-is, or a Sile which contains the grid.

argv : list of str

the arguments passed to sgeom

ret_grid : bool (False)

whether the function should return the grid