ncSileSiesta

class sisl.io.siesta.ncSileSiesta(filename, mode='r', lvl=0, access=1, *args, **kwargs)

Bases: sisl.io.siesta.SileCDFSiesta

Generic NetCDF output file containing a large variety of information

Attributes

__dict__
__doc__
__module__
__weakref__	list of weak references to the object (if defined)
_cmp_args	Returns the compression arguments for the NetCDF file
_write_default
_write_default_only
base_file	File of the current Sile
file	File of the current Sile
grids	Return a list of available grids in this file.

Methods

_ArgumentParser_args_single()	Default arguments for the Sile
__delattr__	Implement delattr(self, name).
__dir__	Default dir() implementation.
__enter__()	Opens the output file and returns it self
__eq__	Return self==value.
__exit__(type, value, traceback)
__format__	Default object formatter.
__ge__	Return self>=value.
__getattr__(name)	Override to check the handle
__getattribute__	Return getattr(self, name).
__gt__	Return self>value.
__hash__	Return hash(self).
__init__(filename[, mode, lvl, access])	Initialize self.
__init_subclass__	This method is called when a class is subclassed.
__iter__([group, dimension, variable, …])	Iterator on all groups, variables and dimensions.
__le__	Return self<=value.
__lt__	Return self<value.
__ne__	Return self!=value.
__new__	Create and return a new object.
__reduce__	Helper for pickle.
__reduce_ex__	Helper for pickle.
__repr__	Return repr(self).
__setattr__	Implement setattr(self, name, value).
__sizeof__	Size of object in memory, in bytes.
__str__()	Return a representation of the Sile
__subclasshook__	Abstract classes can override this to customize issubclass().
_base_file(f)	Make f refer to the file with the appropriate base directory
_base_setup(*args, **kwargs)	Setup the Sile after initialization
_crt_dim(n, name, l)
_crt_grp(n, name)
_crt_var(n, name, *args, **kwargs)
_dimension(name[, tree])	Local method for obtaing the dimension in a certain tree
_dimensions(n, name[, tree])	Retrieve method to get the NetCDF variable
_read_class(cls[, dim])
_read_class_spin(cls, **kwargs)
_setup(*args, **kwargs)	Setup the Sile after initialization
_value(name[, tree])	Local method for obtaining the data from the SileCDF.
_variable(name[, tree])	Local method for obtaining the data from the SileCDF.
_variables(n, name[, tree])	Retrieve method to get the NetCDF variable
_write_overlap(spgroup, csr, orthogonal, S_idx)
_write_settings()	Internal method for writing settings.
_write_sparsity(csr, nsc)
close()
dir_file([filename])	File of the current Sile
exist()	Query whether the file exists
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_basis()	Returns a set of atoms corresponding to the basis-sets in the nc file
read_density_matrix(**kwargs)	Returns a density matrix from the underlying NetCDF file
read_dynamical_matrix(**kwargs)	Returns a dynamical matrix from the underlying NetCDF file
read_energy_density_matrix(**kwargs)	Returns energy density matrix from the underlying NetCDF file
read_fermi_level()	Returns the fermi-level
read_force()	Returns a vector with final forces contained.
read_force_constant()	Reads the force-constant stored in the nc file
read_geometry()	Returns Geometry object from a Siesta.nc file
read_grid(name[, spin])	Reads a grid in the current Siesta.nc file
read_hamiltonian(**kwargs)	Returns a Hamiltonian from the underlying NetCDF file
read_overlap(**kwargs)	Returns a overlap matrix from the underlying NetCDF file
read_supercell()	Returns a SuperCell object from a Siesta.nc file
read_supercell_nsc()	Returns number of supercell connections
write(*args, **kwargs)	Generic write method which should be overloaded in child-classes
write_basis(atom)	Write the current atoms orbitals as the basis
write_density_matrix(DM, **kwargs)	Writes density matrix model to file
write_dynamical_matrix(D, **kwargs)	Writes dynamical matrix model to file
write_energy_density_matrix(EDM, **kwargs)	Writes energy density matrix model to file
write_geometry(geometry)	Creates the NetCDF file and writes the geometry information
write_hamiltonian(H, **kwargs)	Writes Hamiltonian model to file
write_overlap(S, **kwargs)	Write the overlap matrix to the NetCDF file

property base_file

File of the current Sile

close()

dir_file(filename=None)

File of the current Sile

exist()

Query whether the file exists

property file

File of the current Sile

property grids

Return a list of available grids in this file.

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:

1. Group

2. Dimensions in group

3. 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 instances

• dimension (bool (True)) – whether the iterator yields Dimension instances

• variable (bool (True)) – whether the iterator yields Variable instances

• levels (int (-1)) – number of levels to traverse, with respect to root 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

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_basis()

Returns a set of atoms corresponding to the basis-sets in the nc file

read_density_matrix(**kwargs)

Returns a density matrix from the underlying NetCDF file

read_dynamical_matrix(**kwargs)

Returns a dynamical matrix from the underlying NetCDF file

This assumes that the dynamical matrix is stored in the field “H” as would the Hamiltonian. This is counter-intuitive but is required when using PHtrans.

read_energy_density_matrix(**kwargs)

Returns energy density matrix from the underlying NetCDF file

read_fermi_level()

Returns the fermi-level

read_force()

Returns a vector with final forces contained.

read_force_constant()

Reads the force-constant stored in the nc file

Returns

force constants – contains the directions, and 3rd dimensions contains -/+ displacements.

Return type

numpy.ndarray with 5 dimensions containing all the forces. The 2nd dimensions contains

read_geometry()

Returns Geometry object from a Siesta.nc file

read_grid(name, spin=0, **kwargs)

Reads a grid in the current Siesta.nc file

Enables the reading and processing of the grids created by Siesta

Parameters

• name (str) – name of the grid variable to read

• spin (int or array_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.

read_hamiltonian(**kwargs)

Returns a Hamiltonian from the underlying NetCDF file

read_overlap(**kwargs)

Returns a overlap matrix from the underlying NetCDF file

read_supercell()

Returns a SuperCell object from a Siesta.nc file

read_supercell_nsc()

Returns number of supercell connections

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.

write_basis(atom)

Write the current atoms orbitals as the basis

Parameters

atom (Atoms) – atom specifications to write.

write_density_matrix(DM, **kwargs)

Writes density matrix model to file

Parameters

DM (DensityMatrix) – the model to be saved in the NC file

write_dynamical_matrix(D, **kwargs)

Writes dynamical matrix model to file

Parameters

D (DynamicalMatrix) – the model to be saved in the NC file

write_energy_density_matrix(EDM, **kwargs)

Writes energy density matrix model to file

Parameters

EDM (EnergyDensityMatrix) – the model to be saved in the NC file

write_geometry(geometry)

Creates the NetCDF file and writes the geometry information

write_hamiltonian(H, **kwargs)

Writes Hamiltonian model to file

Parameters

• H (Hamiltonian) – the model to be saved in the NC file

• Ef (float, optional) – the Fermi level of the electronic structure (in eV), default to 0.

write_overlap(S, **kwargs)

Write the overlap matrix to the NetCDF file