sisl.Grid

class sisl.Grid(shape, bc=None, lattice: Lattice | None = None, dtype=None, geometry: Geometry | None = None)

Bases: LatticeChild, _Dispatchs

Real-space grid information with associated geometry.

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

Parameters:

shape (float or (3,) of int) – the shape of the grid. A float specifies the grid spacing in Angstrom, while a list of integers specifies the exact grid size.
bc (list of int (3, 2) or (3, ), optional) – the boundary conditions for each of the cell’s planes. Default to periodic BC.
lattice – the lattice that this grid represents. lattice has precedence if both geometry and lattice has been specified. Defaults to [1, 1, 1].
dtype (numpy.dtype, optional) – the data-type of the grid, default to numpy.float64.
geometry – associated geometry with the grid. If lattice has not been passed the lattice will be taken from this geometry.

Examples

>>> grid1 = Grid(0.1, lattice=10)
>>> grid2 = Grid(0.1, lattice=Lattice(10))
>>> grid3 = Grid(0.1, lattice=Lattice([10] * 3))
>>> grid1 == grid2
True
>>> grid1 == grid3
True
>>> grid = Grid(0.1, lattice=10, dtype=np.complex128)
>>> grid == grid1
False

It is possible to provide a geometry and a different lattice to make a smaller (or bigger) lattice based on a geometry. This might be useful when creating wavefunctions or expanding densities to grids. Here we create a square grid based on a hexagonal graphene lattice. Expanding wavefunctions from this geometry will automatically convert to the lattice size. >>> lattice = Lattice(10) # square lattice 10x10x10 Ang >>> geometry = geom.graphene() >>> grid = Grid(0.1, lattice=lattice, geometry=geometry)

Methods

`append`(other, axis)	Appends other `Grid` to this grid along axis
`apply`(function_, args, *kwargs)	Applies a function to the grid and returns a new grid
`area`(ax0, ax1)	Calculate the area spanned by the two axis ax0 and ax1
`average`(axis[, weights])	Average grid values along direction axis.
`copy`([dtype])	Copy the object, possibly changing the data-type
`cross_section`(idx, axis)	Takes a cross-section of the grid along axis axis
`fill`(val)	Fill the grid with this value
`index`(coord[, axis])	Find the grid index for a given coordinate (possibly only along a given lattice vector axis)
`index2xyz`(index)	Real-space coordinates of indices related to the grid
`index_fold`(index[, unique])	Converts indices from any placement to only exist in the "primary" grid
`index_truncate`(index)	Remove indices from outside the grid to only retain indices in the "primary" grid
`interp`(shape[, order, mode])	Interpolate grid values to a new resolution (retaining lattice vectors)
`isosurface`(level[, step_size])	Calculates the isosurface for a given value
`mean`(axis[, weights])	Average grid values along direction axis.
`mgrid`(*slices)	Return a list of indices corresponding to the slices
`pyamg_boundary_condition`(A, b)	Attach boundary conditions to the pyamg grid-matrix A with default boundary conditions as specified for this `Grid`
`pyamg_fix`(A, b, pyamg_indices, value)	Fix values for the stencil to value.
`pyamg_index`(index)	Calculate pyamg matrix indices from a list of grid indices
`pyamg_source`(b, pyamg_indices, value)	Fix the source term to value.
`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 `Lattice.sc_index` function
`set_bc`(bc)
`set_boundary`(bc)
`set_boundary_condition`(bc)
`set_geometry`(geometry[, also_lattice])	Sets the `Geometry` for the grid.
`set_grid`(shape[, dtype])	Create the internal grid of certain size.
`set_lattice`(lattice)	Overwrites the local lattice.
`set_nsc`(args, *kwargs)	Set the number of super-cells in the `Lattice` object
`set_supercell`(lattice)	Overwrites the local lattice.
`smooth`([r, method, mode])	Make a smoother grid by applying a filter
`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)	Sum grid values along axis axis.
`swapaxes`(axis1, axis2)	Swap two axes in the grid (also swaps axes in the lattice)
`tile`(reps, axis)	Tile grid to create a bigger one
`topyamg`([dtype])	Create a pyamg stencil matrix to be used in pyamg
`write`(sile, args, *kwargs)	Writes grid to the sile using sile.write_grid
`DIRICHLET`
`NEUMANN`
`OPEN`
`PERIODIC`
`boundary_condition`
`cell`	Returns the inherent `Lattice.cell`
`dcell`	Voxel cell size
`dkind`	The data-type of the grid (in str)
`dtype`	Data-type used in grid
`dvolume`	Volume of the grid voxel elements
`icell`	Returns the inherent `Lattice.icell`
`isc_off`	Returns the inherent `Lattice.isc_off`
`length`	Returns the inherent `Lattice.length`
`n_s`	Returns the inherent `Lattice.n_s`
`new`
`nsc`	Returns the inherent `Lattice.nsc`
`origin`	Returns the inherent `Lattice.origin`
`pbc`
`plot`	Handles all plotting possibilities for a class
`rcell`	Returns the inherent `Lattice.rcell`
`sc`	[deprecated] Return the lattice object associated with the `Lattice`.
`sc_off`	Returns the inherent `Lattice.sc_off`
`shape`	Grid shape in \(x\), \(y\), \(z\) directions
`size`	Total number of elements in the grid
`to`	A dispatcher for classes, using __get__ it converts into ObjectDispatcher upon invocation from an object, or a TypeDispatcher when invoked from a class
`volume`	Returns the inherent `Lattice.volume`

DIRICHLET = 3

NEUMANN = 4

OPEN = 5

PERIODIC = 2

__init__(shape, bc=None, lattice: Lattice | None = None, dtype=None, geometry: Geometry | None = None)[source]

append(other: GridLike, axis: CellAxis) → Grid: Appends other Grid to this grid along axis

apply(function_, *args, **kwargs)

Applies a function to the grid and returns a new grid

You can also apply a function that does not return a grid (maybe you want to do some measurement). In that case, you will get the result instead of a Grid.

Parameters:

function (str or function) – for a string the full module path to the function should be given. The function that will be called should have the grid as the first argument in its interface.
**kwargs (*args and) –
arguments that go directly to the function call

Notes

The function argument name function_ is named so that function can be an eligible keyword argument for the function.

area(ax0, ax1) → float: Calculate the area spanned by the two axis ax0 and ax1

average(axis, weights=None)[source]

Average grid values along direction axis.

Parameters:

axis (int) – unit-cell direction to average across
weights (array_like, optional) – the weights for the individual axis elements, if boolean it corresponds to 0 and 1 for false/true.

See also

numpy.average: for details regarding the weights argument

property boundary_condition: ndarray

property cell: ndarray: Returns the inherent Lattice.cell

copy(dtype=None) → Grid: Copy the object, possibly changing the data-type

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

property dcell: Voxel cell size

property dkind: The data-type of the grid (in str)

property dtype: Data-type used in grid

property dvolume: Volume of the grid voxel elements

fill(val)[source]

Fill the grid with this value

Parameters:: val (numpy.dtype) – all grid-points will have this value after execution

property icell: ndarray: Returns the inherent Lattice.icell

index(coord, axis=None)[source]

Find the grid index for a given coordinate (possibly only along a given lattice vector axis)

Parameters:

coord ((:, 3) or float or Shape) – the coordinate of the axis. If a float is passed axis is also required in which case it corresponds to the length along the lattice vector corresponding to axis. If a Shape a list of coordinates that fits the voxel positions are returned (all internal points also).
axis (int, optional) – the axis direction of the index, or for all axes if none.

index2xyz(index)[source]

Real-space coordinates of indices related to the grid

Parameters:: index (array_like) – indices for grid-positions
Returns:: coordinates of the indices with respect to this grid spacing
Return type:: numpy.ndarray

index_fold(index, unique=True)[source]

Converts indices from any placement to only exist in the “primary” grid

Examples

>>> grid = Grid([10, 10, 10])
>>> assert np.all(grid.index_fold([-1, -1, -1]) == 9)

Parameters:

index (array_like) – indices for grid-positions
unique (bool, optional) – if true the returned indices are made unique after having folded the index points

Returns:

all indices are then within the shape of the grid

Return type:

numpy.ndarray

See also

index_truncate: truncate indices by removing indices outside the primary cell

index_truncate(index)[source]

Remove indices from outside the grid to only retain indices in the “primary” grid

Examples

>>> grid = Grid([10, 10, 10])
>>> assert len(grid.index_truncate([-1, -1, -1])) == 0

Parameters:: index (array_like) – indices for grid-positions
Returns:: all indices are then within the shape of the grid (others have been removed
Return type:: numpy.ndarray

See also

index_fold: fold indices into the primary cell

interp(shape, order=1, mode='wrap', **kwargs)[source]

Interpolate grid values to a new resolution (retaining lattice vectors)

It uses the scipy.ndimage.zoom, which creates a finer or more spaced grid using spline interpolation. The lattice vectors remains unchanged.

Parameters:

shape (int, array_like of len 3) – the new shape of the grid.
order (int 0-5, optional) – the order of the spline interpolation. 1 means linear, 2 quadratic, etc…
mode ({'wrap', 'mirror', 'constant', 'reflect', 'nearest'}) – determines how to compute the borders of the grid. The default is 'wrap', which accounts for periodic conditions.
**kwargs – optional arguments passed to the interpolation algorithm The interpolation routine is scipy.ndimage.zoom

See also

scipy.ndimage.zoom: method used for interpolation

property isc_off: ndarray: Returns the inherent Lattice.isc_off

isosurface(level: float, step_size: int = 1, **kwargs)[source]

Calculates the isosurface for a given value

It uses skimage.measure.marching_cubes, so you need to have scikit-image installed.

Parameters:

level – contour value to search for isosurfaces in the grid. If not given or None, the average of the min and max of the grid is used.
step_size – step size in voxels. Larger steps yield faster but coarser results. The result will always be topologically correct though.
**kwargs – optional arguments passed directly to skimage.measure.marching_cubes for the calculation of isosurfaces.

Returns:

numpy array of shape (V, 3) – Verts. Spatial coordinates for V unique mesh vertices.
numpy array of shape (n_faces, 3) – Faces. Define triangular faces via referencing vertex indices from verts. This algorithm specifically outputs triangles, so each face has exactly three indices.
numpy array of shape (V, 3) – Normals. The normal direction at each vertex, as calculated from the data.
numpy array of shape (V, 3) – Values. Gives a measure for the maximum value of the data in the local region near each vertex. This can be used by visualization tools to apply a colormap to the mesh.

See also

skimage.measure.marching_cubes: method used to calculate the isosurface.

property length: float: Returns the inherent Lattice.length

mean(axis, weights=None)

Average grid values along direction axis.

Parameters:

axis (int) – unit-cell direction to average across
weights (array_like, optional) – the weights for the individual axis elements, if boolean it corresponds to 0 and 1 for false/true.

See also

numpy.average: for details regarding the weights argument

classmethod mgrid(*slices)[source]

Return a list of indices corresponding to the slices

The returned values are equivalent to numpy.mgrid but they are returned in a (:, 3) array.

Parameters:: *slices (slice or list of int or int) – return a linear list of indices that points to the collective slice made by the passed arguments
Returns:: linear indices for each of the sliced values, shape (*, 3)
Return type:: numpy.ndarray

property n_s: int: Returns the inherent Lattice.n_s

new = <TypeDispatcher{obj=<class 'sisl.Grid'>}>

property nsc: ndarray: Returns the inherent Lattice.nsc

property origin: ndarray: Returns the inherent Lattice.origin

property pbc: ndarray

plot: Handles all plotting possibilities for a class

pyamg_boundary_condition(A, b)[source]

Attach boundary conditions to the pyamg grid-matrix A with default boundary conditions as specified for this Grid

Parameters:

A (scipy.sparse.csr_matrix) – sparse matrix describing the grid
b (numpy.ndarray) – a vector containing RHS of \(A x = b\) for the solution of the grid stencil

pyamg_fix(A, b, pyamg_indices, value)[source]

Fix values for the stencil to value.

Parameters:

A (csr_matrix/csc_matrix) – sparse matrix describing the LHS for the linear system of equations
b (numpy.ndarray) – a vector containing RHS of \(A x = b\) for the solution of the grid stencil
pyamg_indices (list of int) – the linear pyamg matrix indices where the value of the grid is fixed. I.e. the indices should correspond to returned quantities from pyamg_indices.
value (float) – the value of the grid to fix the value at

pyamg_index(index)[source]

Calculate pyamg matrix indices from a list of grid indices

Parameters:: index ((:, 3) of int) – a list of indices of the grid along each grid axis
Returns:: linear indices for the matrix
Return type:: numpy.ndarray

See also

index: query indices from coordinates (directly passable to this method)
mgrid: Grid equivalent to numpy.mgrid. Grid.mgrid returns indices in shapes (:, 3), contrary to numpy’s numpy.mgrid

Raises:: ValueError – if any of the passed indices are below 0 or above the number of elements per axis

classmethod pyamg_source(b, pyamg_indices, value)[source]

Fix the source term to value.

Parameters:

b (numpy.ndarray) – a vector containing RHS of \(A x = b\) for the solution of the grid stencil
pyamg_indices (list of int) – the linear pyamg matrix indices where the value of the grid is fixed. I.e. the indices should correspond to returned quantities from pyamg_indices.

property rcell: ndarray: Returns the inherent Lattice.rcell

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

Reads grid from the Sile using read_grid

Parameters:

sile (Sile, str or pathlib.Path) – 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: int | Sequence[int], axis: Literal[0, 1, 2, 'a', 'b', 'c']) → Grid

Removes certain indices from a specified axis.

Works exactly opposite to sub.

Parameters:

idx – the indices of the grid axis axis to be removed
axis – 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 (int) – the index 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:,...]

property sc: [deprecated] Return the lattice object associated with the Lattice.

sc_index(*args, **kwargs) → int | Sequence[int]: Call local Lattice.sc_index function

property sc_off: ndarray: Returns the inherent Lattice.sc_off

set_bc(bc)[source]

set_boundary(bc)[source]

set_boundary_condition(bc)[source]

set_geometry(geometry, also_lattice: bool = True)[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, so passing None is a viable option.

Parameters:

geometry (Geometry or None) – specify the new geometry in the Grid. If None will remove the geometry (but not the lattice)
also_lattice (bool, optional) – whether to also set the lattice for the grid according to the lattice of the geometry, if False it will keep the lattice as it was.

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

set_lattice(lattice): Overwrites the local lattice.

set_nsc(*args, **kwargs)

Set the number of super-cells in the Lattice object

See set_nsc for allowed parameters.

See also

Lattice.set_nsc: the underlying called method

set_supercell(lattice): Overwrites the local lattice.

property shape: Grid shape in \(x\), \(y\), \(z\) directions

property size: Total number of elements in the grid

smooth(r=0.7, method='gaussian', mode='wrap', **kwargs)[source]

Make a smoother grid by applying a filter

Parameters:

r (float or array-like of len 3, optional) –
the radius of the filter in Angstrom for each axis. If the method is "gaussian", this is the standard deviation!

If a single float is provided, then the same distance will be used for all axes.
method ({'gaussian', 'uniform'}) – the type of filter to apply to smoothen the grid.
mode ({'wrap', 'mirror', 'constant', 'reflect', 'nearest'}) – determines how to compute the borders of the grid. The default is wrap, which accounts for periodic conditions.

See also

scipy.ndimage.gaussian_filter

sub(idx: int | Sequence[int], axis: Literal[0, 1, 2, 'a', 'b', 'c']) → Grid

Retains certain indices from a specified axis.

Works exactly opposite to remove.

Parameters:

idx – the indices of the grid axis axis to be retained
axis – 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 (int) – the index 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]

Sum grid values along axis axis.

Parameters:: axis (int) – unit-cell direction to sum across

swapaxes(axis1: Literal[0, 1, 2, 'a', 'b', 'c'], axis2: Literal[0, 1, 2, 'a', 'b', 'c']) → Grid

Swap two axes in the grid (also swaps axes in the lattice)

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

Parameters:

axis1 – axes indices to be swapped
axis2 – axes indices to be swapped

tile(reps: int, axis: Literal[0, 1, 2, 'a', 'b', 'c']) → Grid

Tile grid to create a bigger one

The atomic indices for the base Geometry will be retained.

Parameters:

reps – number of tiles (repetitions)
axis – direction of tiling, 0, 1, 2 according to the cell-direction

:raises SislError : when the lattice is not commensurate with the geometry:

See also

Geometry.tile: equivalent method for Geometry class

to

A dispatcher for classes, using __get__ it converts into ObjectDispatcher upon invocation from an object, or a TypeDispatcher when invoked from a class

This is a class-placeholder allowing a dispatcher to be a class attribute and converted into an ObjectDispatcher when invoked from an object.

If it is called on the class, it will return a TypeDispatcher.

This class should be an attribute of a class. It heavily relies on the __get__ special method.

Parameters:

name (str) – name of the attribute in the class
dispatchs (dict, optional) – dictionary of dispatch methods
obj_getattr (callable, optional) – method with 2 arguments, an obj and the attr which may be used to control how the attribute is called.
instance_dispatcher (AbstractDispatcher, optional) – control how instance dispatchers are handled through __get__ method. This controls the dispatcher used if called from an instance.
type_dispatcher (AbstractDispatcher, optional) – control how class dispatchers are handled through __get__ method. This controls the dispatcher used if called from a class.

Examples

>>> class A:
...   new = ClassDispatcher("new", obj_getattr=lambda obj, attr: getattr(obj.sub, attr))

The above defers any attributes to the contained A.sub attribute.

topyamg(dtype=None)[source]

Create a pyamg stencil matrix to be used in pyamg

This allows retrieving the grid matrix equivalent of the real-space grid. Subsequently the returned matrix may be used in pyamg for solutions etc.

The pyamg suite is it-self a rather complicated code with many options. For details we refer to pyamg.

Parameters:

dtype (numpy.dtype, optional) – data-type used for the sparse matrix, default to use the grid data-type

Returns:

scipy.sparse.csr_matrix – the stencil for the pyamg solver
numpy.ndarray – RHS of the linear system of equations

Examples

This example proves the best method for a variety of cases in regards of the 3D Poisson problem:

>>> grid = Grid(0.01)
>>> A, b = grid.topyamg() # automatically setups the current boundary conditions
>>> # add terms etc. to A and/or b
>>> import pyamg
>>> from scipy.sparse.linalg import cg
>>> ml = pyamg.aggregation.smoothed_aggregation_solver(A, max_levels=1000)
>>> M = ml.aspreconditioner(cycle='W') # pre-conditioner
>>> x, info = cg(A, b, tol=1e-12, M=M)

See also

pyamg_index: convert grid indices into the sparse matrix indices for A
pyamg_fix: fixes stencil for indices and fixes the source for the RHS matrix (uses pyamg_source)
pyamg_source: fix the RHS matrix b to a constant value
pyamg_boundary_condition: setup the sparse matrix A to given boundary conditions (called in this routine)

property volume: float: Returns the inherent Lattice.volume

write(sile: SileLike, *args, **kwargs) → None

Writes grid to the sile using sile.write_grid

Parameters:

sile – 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
*args – Any other args will be passed directly to the underlying routine
**kwargs – Any other args will be passed directly to the underlying routine

See also

Grid.read: reads a Grid from a given Sile/file