Brillouin zone
The Brillouin zone objects are all special classes enabling easy manipulation of an underlying physical quantity.
Quite often a physical quantity will be required to be averaged, or calculated individually over a number of kpoints. In this regard the Brillouin zone objects can help.
The BrillouinZone object allows direct looping of contained kpoints while invoking particular methods from the contained object. This is best shown with an example:
>>> H = Hamiltonian(...)
>>> bz = BrillouinZone(H)
>>> bz.apply.array.eigh()
This will calculate eigenvalues for all kpoints associated with the BrillouinZone
and
return everything as an array. The dispatch property of
the BrillouinZone
object has several use cases (here array
is shown).
This may be extremely convenient when calculating bandstructures:
>>> H = Hamiltonian(...)
>>> bs = BandStructure(H, [[0, 0, 0], [0.5, 0, 0]], 100)
>>> bs_eig = bs.apply.array.eigh()
>>> plt.plot(bs.lineark(), bs_eig)
and then you have all eigenvalues for all the kpoints along the path.
Multiple quantities
Sometimes one may want to postprocess the data for each kpoint. As an example lets postprocess the DOS on a per kpoint basis while calculating the average:
>>> H = Hamiltonian(...)
>>> mp = MonkhorstPack(H, [10, 10, 10])
>>> E = np.linspace(2, 2, 100)
>>> def wrap_DOS(eigenstate):
... # Calculate the DOS for the eigenstates
... DOS = eigenstate.DOS(E)
... # Calculate the velocity for the eigenstates
... v = eigenstate.velocity()
... V = (v ** 2).sum(1)
... return DOS.reshape(1, 1) * v ** 2 / V.reshape(1, 1)
>>> DOS = mp.apply.average.eigenstate(wrap=wrap_DOS, eta=True)
This will, calculate the Monkhorst pack kaveraged DOS split into 3 Cartesian
directions based on the eigenstates velocity direction. This method of manipulating
the result can be extremely powerful to calculate many quantities while running an
efficient BrillouinZone
average. The eta flag will print, to stdout, a progressbar.
The usage of the wrap
method are also passed optional arguments, parent
which is
H
in the above example. k
and weight
are the current kpoint and weight of the
corresponding kpoint. An example could be to manipulate the DOS depending on the kpoint and
weight:
>>> H = Hamiltonian(...)
>>> mp = MonkhorstPack(H, [10, 10, 10])
>>> E = np.linspace(2, 2, 100)
>>> def wrap_DOS(eigenstate, k, weight):
... # Calculate the DOS for the eigenstates and weight by k_x and weight
... return eigenstate.DOS(E) * k[0] * weight
>>> DOS = mp.apply.sum.eigenstate(wrap=wrap_DOS, eta=True)
When using wrap to calculate more than one quantity per eigenstate it may be advantageous
to use oplist
to handle cases of BrillouinZone.apply.average and BrillouinZone.apply.sum.
>>> H = Hamiltonian(...)
>>> mp = MonkhorstPack(H, [10, 10, 10])
>>> E = np.linspace(2, 2, 100)
>>> def wrap_multiple(eigenstate):
... # Calculate DOS/PDOS for eigenstates
... DOS = eigenstate.DOS(E)
... PDOS = eigenstate.PDOS(E)
... # Calculate velocity for the eigenstates
... v = eigenstate.velocity()
... return oplist([DOS, PDOS, v])
>>> DOS, PDOS, v = mp.apply.average.eigenstate(wrap=wrap_multiple, eta=True)
Which does mathematical operations (averaging/summing) using oplist
.
In some cases quantities are needed for all \(k\) points and in such cases
it may not always be that the returned quantities are commensurate.
Lets reuse the previous wrap_multiple
function and try and return the
full quantity:
>>> DOS_PDOS_v = mp.apply.eigenstate(wrap=wrap_multiple, eta=True)
This will raise an error since wrap_multiple
returns an oplist (same as a list)
and thus is unable to convert this into an equivalent numpy.ndarray
. Additionally
this can not be merged together in a single numpy.ndarray
since the shapes of the returned
quantities are not commensurate. One cannot concatenate the 3 different quantities.
To accomblish this one may use an zip
flag where the two lines are equivalent:
>>> DOS, PDOS, v = mp.apply.array.renew(zip=True).eigenstate(wrap=wrap_multiple, eta=True)
>>> DOS, PDOS, v = mp.apply(zip=True).array.eigenstate(wrap=wrap_multiple, eta=True)
and the data is unpacked as wanted.
Parallel calculations
The apply
method looping kpoints may be explicitly parallelized.
To run parallel do:
>>> H = Hamiltonian(...)
>>> mp = MonkhorstPack(H, [10, 10, 10])
>>> with mp.apply.renew(pool=True) as par:
... par.eigh()
This requires you also have the package pathos
available.
The above will run in parallel using a default number of processors
in priority:
Environment variable
SISL_NUM_PROCS
Return value of
os.cpu_count()
.
Note that this may interfere with BLAS implementation which defaults
to use all CPU’s for threading. The total processors/threads that will
be created is SISL_NUM_PROCS * OMP_NUM_THREADS
. Try and ensure this is below
the actual corecount of your machine (or the number of requested cores in a
HPC environment).
Alternatively one can control the number of processors locally by doing:
>>> H = Hamiltonian(...)
>>> mp = MonkhorstPack(H, [10, 10, 10])
>>> with mp.apply.renew(pool=2) as par:
... par.eigh()
which will request 2 processors (regardless of corecount).
As a last resort you can pass your own Pool
of workers that
will be used for the parallel processing.
>>> from multiprocessing import Pool
>>> pool = Pool(4)
>>> H = Hamiltonian(...)
>>> mp = MonkhorstPack(H, [10, 10, 10])
>>> with mp.apply.renew(pool=pool) as par:
... par.eigh()
The Pool
should implement some standard methods that are
existing in the pathos
enviroment such as Pool.restart
and Pool.terminate
and imap
and uimap
methods. See the pathos
documentation for detalis.

A class to construct Brillouin zone related quantities 

Create a MonkhorstPack grid for the Brillouin zone 

Create a path in the Brillouin zone for plotting bandstructures etc. 