nbodykit.source.mesh.linear¶

Classes

LinearMesh(Plin, BoxSize, Nmesh[, seed, ...])

A MeshSource object that generates a RealField density mesh from a linear power spectrum function \(P(k)\).

class nbodykit.source.mesh.linear.LinearMesh(Plin, BoxSize, Nmesh, seed=None, unitary_amplitude=False, inverted_phase=False, remove_variance=None, comm=None)[source]¶

A MeshSource object that generates a RealField density mesh from a linear power spectrum function \(P(k)\).

Parameters

Plin (callable) – the callable linear power spectrum function, which takes the wavenumber as its single argument
BoxSize (float, 3-vector of floats) – the size of the box to generate the grid on
Nmesh (int, 3-vector of int) – the number of the mesh cells per side
seed (int, optional) – the global random seed, used to set the seeds across all ranks
remove_variance (bool, optional) –

Deprecated since version 0.2.9: use unitary_amplitude instead
unitary_amplitude (bool, optional) – True to remove variance from the complex field by fixing the amplitude to \(P(k)\) and only the phase is random.
inverted_phase (bool, optional) – True to invert phase of the complex field by fixing the amplitude to \(P(k)\) and only the phase is random.
comm (MPI communicator) – the MPI communicator

Attributes

actions: A list of actions to apply to the density field when interpolating to the mesh.
attrs: A dictionary storing relevant meta-data about the CatalogSource.

Methods

`apply`(func[, kind, mode])	Return a view of the mesh, with `actions` updated to apply the specified function, either in Fourier space or configuration space, based on `mode`
`compute`([mode, Nmesh])	Compute / Fetch the mesh object into memory as a RealField or ComplexField object.
`preview`([axes, Nmesh, root])	Gather the mesh into as a numpy array, with (reduced) resolution.
`save`(output[, dataset, mode])	Save the mesh as a `BigFileMesh` on disk, either in real or complex space.
`to_complex_field`()	Return a ComplexField, generating from the linear power spectrum.
`to_field`([mode, out])	Return the mesh as a `pmesh` Field object, either in Fourier space or configuration space, based on `mode`.
`to_real_field`([out, normalize])	Convert the mesh source to the configuration-space field, returning a `pmesh.pm.RealField` object.
`view`()	Return a "view" of the MeshSource, in the spirit of numpy's ndarray view.

paint

__finalize__(other)¶

Finalize the creation of a MeshSource object by copying over attributes from a second MeshSource.

Parameters: other (MeshSource) – the second MeshSource to copy over attributes from

__len__()¶: Length of a mesh source is zero

property actions¶

A list of actions to apply to the density field when interpolating to the mesh.

This stores tuples of (mode, func, kind); see apply() for more details.

apply(func, kind='wavenumber', mode='complex')¶

Return a view of the mesh, with actions updated to apply the specified function, either in Fourier space or configuration space, based on mode

Parameters

func (callable or a MeshFilter object) – func(x, y) where x is a list of r (k) values that broadcasts into a full array, when mode is ‘real’ (‘complex’); the value of x depends on kind. y is the value of the mesh field on the corresponding locations.
kind (string, optional) –
if a MeshFilter object is given as func, this is ignored. The kind of value in x.
- When mode is ‘complex’:
  - ’wavenumber’ means wavenumber from [- 2 pi / L * N / 2, 2 pi / L * N / 2).
  - ’circular’ means circular frequency from [- pi, pi).
  - ’index’ means [0, Nmesh )
- When mode is ‘real’:
  - ’relative’ means distance from [-0.5 Boxsize, 0.5 BoxSize).
  - ’index’ means [0, Nmesh )
mode ('complex' or 'real', optional) – if a MeshFilter object is given as func, this is ignored. whether to apply the function to the mesh in configuration space or Fourier space

Returns

a view of the mesh object with the actions attribute updated to include the new action

Return type

MeshSource

property attrs¶: A dictionary storing relevant meta-data about the CatalogSource.

compute(mode='real', Nmesh=None)¶: Compute / Fetch the mesh object into memory as a RealField or ComplexField object.

preview(axes=None, Nmesh=None, root=0)¶

Gather the mesh into as a numpy array, with (reduced) resolution. The result is broadcast to all ranks, so this uses \(\mathrm{Nmesh}^3\) per rank.

Parameters

Nmesh (int, array_like) – The desired Nmesh of the result. Be aware this function allocates memory to hold a full Nmesh on each rank.
axes (int, array_like) – The axes to project the preview onto., e.g. (0, 1)
root (int, optional) – the rank number to treat as root when gathering to a single rank

Returns

out – An numpy array holding the real density field.

Return type

array_like

save(output, dataset='Field', mode='real')¶

Save the mesh as a BigFileMesh on disk, either in real or complex space.

Parameters

output (str) – name of the bigfile file
dataset (str, optional) – name of the bigfile data set where the field is stored
mode (str, optional) – real or complex; the form of the field to store

to_complex_field()[source]¶

Return a ComplexField, generating from the linear power spectrum.

Note

The density field is normalized to \(1+\delta\) such that the mean of the return field in real space is unity.

Returns: an array-like object holding the generated linear density field in Fourier space
Return type: pmesh.pm.ComplexField

to_field(mode='real', out=None)¶

Return the mesh as a pmesh Field object, either in Fourier space or configuration space, based on mode.

This will call to_real_field() or to_complex_field() based on mode.

Parameters: mode ('real' or 'complex') – the return type of the field
Returns: either a RealField of ComplexField, storing the value of the field on the mesh
Return type: RealField, ComplexField

to_real_field(out=None, normalize=True)¶

Convert the mesh source to the configuration-space field, returning a pmesh.pm.RealField object.

Not implemented in the base class, unless object is a view.

view()¶

Return a “view” of the MeshSource, in the spirit of numpy’s ndarray view.

This returns a new MeshSource whose memory is owned by self.

Note that for CatalogMesh objects, this is overidden by the CatalogSource.view function.