 documentation fixups prior to release

parent decfecfe
 ... ... @@ -60,14 +60,9 @@ #HIDDEN_BEGIN_yvri def plot_spectrum(syst, Bfields): # In the following, we compute the spectrum of the quantum dot # using dense matrix methods. This works in this toy example, as # the system is tiny. In a real example, one would want to use # sparse matrix methods energies = [] for B in Bfields: # Obtain the Hamiltonian as a dense matrix # Obtain the Hamiltonian as a sparse matrix ham_mat = syst.hamiltonian_submatrix(params=dict(B=B), sparse=True) # we only calculate the 15 lowest eigenvalues ... ...
 ... ... @@ -83,7 +83,9 @@ Here is an example for extracting the symmetry group of a graphene system:: kwant.qsymm also contains functionality for converting Qsymm models to Kwant Builders, and vice versa, and for working with continuum Hamiltonians (such as would be used with kwant.continuum) kwant.continuum). This integration requires separately installing Qsymm, which is available on the Python Package Index _. Automatic Peierls phase calculation ----------------------------------- ... ... @@ -101,8 +103,7 @@ which calculates the Peierls phases for you:: return -t * peierls(a, b) syst = make_system(hopping) lead = make_lead(hopping) lead.substituted(peierls='peierls_lead') lead = make_lead(hopping).substituted(peierls='peierls_lead') syst.attach_lead(lead) syst = syst.finalized() ... ... @@ -135,19 +136,19 @@ has a parameter V, and one wishes to have different values for V in the scattering region and leads, one could do the following:: syst = kwant.Builder() syst.fill(model.substituted(V='V_dot', ...)) syst.fill(model.substituted(V='V_dot'), ...)) lead = kwant.Builder() lead.fill(model.substituted(V='V_lead'), ...) syst.attach_lead(lead) fsyst = syst.finalized() syst = syst.finalized() kwant.smatrix(syst, params=dict(V_dot=0, V_lead=1)) Interpolated density plots -------------------------- A new function, ~kwant.plotter.density, has been added that can be used to A new function, kwant.plotter.density, has been added that can be used to visualize a density defined over the sites of a Kwant system. This convolves the "discrete" density (defined over the system sites) with a "bump" function in realspace. The output of ~kwant.plotter.density can be more informative ... ... @@ -166,7 +167,8 @@ but in an inconsistent way (e.g. a parameter 'phi' that is a superconducting phase in one value function, but a peierls phase in another). This leads to bugs that are confusing and hard to track down. Concretely, the above means that the following no longer works:: For this reason value functions may no longer have default values for paramters. Concretely this means that the following no longer works:: syst = kwant.Builder() ... ... @@ -190,7 +192,7 @@ To deal with many parameters, the following idiom may be useful:: ... smatrix = kwant.smatrix(syst, E, params=dict(defaults, d=4, e=5)) Note that it allows to override defaults as well as to add additional Note that this allows to override defaults as well as to add additional parameters. System parameters can now be inspected ... ... @@ -228,9 +230,9 @@ This is a provisional API that may be changed in a future version of Kwant. Passing system arguments via args is deprecated in favor of params -------------------------------------------------------------------------- It is now deprecated to pass arguments to systems by providing the args parameter (in kwant.smatrix and elsewhere). This is error prone and requires that all value functions take the same formal parameters, even if they do not depend on all of them. The args parameter (in kwant.smatrix and elsewhere). Passing arguments via args is error prone and requires that all value functions take the same formal parameters, even if they do not depend on all of them. The preferred way of passing parameters to Kwant systems is by passing a dictionary using params:: ... ... @@ -244,7 +246,7 @@ a dictionary using params:: # Compare this to the deprecated 'args' kwant.smatrix(syst, args=(0.5, 0.2)) The ability to provide args will be removed in a future Kwant version. Providing args will be removed in a future Kwant version. Finalized Builders keep track of which sites were added when attaching leads ---------------------------------------------------------------------------- ... ... @@ -261,8 +263,8 @@ that this option is not available in ~kwant.plotter.current. In order to use it, one has to call streamplot directly as shown in the docstring of current. kwant.continuum.discretize can be used with rectangular lattices ---------------------------------------------------------------- kwant.continuum.discretize can be used with rectangular lattices ------------------------------------------------------------------ Previously the discretizer could only be used with lattices with the same lattice constant in all directions. Now it is possible to pass rectangular lattices to the discretizer:: ... ...
 ... ... @@ -4,4 +4,4 @@ .. automodule:: kwant.kpm :members: :special-members: :exclude-members: __weakref__ :exclude-members: __weakref__, __init__
 ... ... @@ -27,5 +27,6 @@ Computation of magnetic field gauge .. autosummary:: :toctree: generated/ :template: autosummary/functor.rst magnetic_gauge
 ... ... @@ -161,8 +161,8 @@ energy eigenstates: .. image:: /code/figure/discretizer_gs.* Note in the above that we pass the spatially varying potential *function* to our system via a parameter called V, because the symbol $V$ was used in the intial, symbolic, definition of the Hamiltonian. to our system via a parameter called V, because the symbol :math:V was used in the initial, symbolic, definition of the Hamiltonian. In addition, the function passed as V expects two input parameters x and y, the same as in the initial continuum Hamiltonian. ... ...
 ... ... @@ -423,7 +423,7 @@ the modes are sorted in the following way: + Positive velocity modes are ordered by *decreasing* momentum For more complicated systems and band structures this can lead to some possibly unintuitive orderings: unintuitive orderings: .. image:: /code/figure/faq_pm2.* ... ... @@ -437,9 +437,9 @@ infinity" (*not* towards the system) which means that the incoming modes are those that have *negative* velocities. This means that for a lead attached on the left of a scattering region (with symmetry vector $(-1, 0)$, for example), the positive $k$ direction (when inspecting the lead's band structure) actually corresponds to the *negative* $x$ direction. symmetry vector :math:(-1, 0), for example), the positive :math:k direction (when inspecting the lead's band structure) actually corresponds to the *negative* :math:x direction. How does Kwant order components of an individual wavefunction? ... ...
 ... ... @@ -112,9 +112,6 @@ in the following piece of code: :start-after: #HIDDEN_BEGIN_zydk :end-before: #HIDDEN_END_zydk Here we use in contrast to the previous example a sparse matrix and the sparse linear algebra functionality of SciPy. The code for computing the band structure and the conductance is identical to the previous examples, and needs not be further explained here. ... ...
 ... ... @@ -340,7 +340,7 @@ vectors Note that the Kubo conductivity must be normalized with the area covered by the vectors. In this case, each local vector represents a site, and covers an area of half a unit cell, while the sum covers one unit cell. It is possible to use random vectors to get an average spectation It is possible to use random vectors to get an average expectation value of the conductivity over large parts of the system. In this case, the area that normalizes the result, is the area covered by the random vectors. ... ...
 ... ... @@ -122,7 +122,7 @@ better for the special case of a square lattice. As our model breaks time reversal symmetry (because of the applied magnetic field) we can also see an intereting property of the eigenstates, namely field) we can also see an interesting property of the eigenstates, namely that they can have *non-zero* local current. We can calculate the local current due to a state by using kwant.operator.Current and plotting it using kwant.plotter.current: ... ...
 ... ... @@ -41,7 +41,7 @@ class SpectralDensity: .. math:: ρ_A(E) = ρ(E) A(E), where :math:ρ(E) = \\sum_{k=0}^{D-1} δ(E-E_k) is the density of where :math:ρ(E) = \sum_{k=0}^{D-1} δ(E-E_k) is the density of states, and :math:A(E) is the expectation value of :math:A for all the eigenstates with energy :math:E. ... ... @@ -253,11 +253,9 @@ class SpectralDensity: Returns ------- (energies, densities) if the energy parameter is not provided, else densities. energies : array of floats Drawn from the nodes of the highest Chebyshev polynomial. Not returned if 'energy' was not provided densities : float or array of floats single float if the energy parameter is a single float, else an array of float. ... ... @@ -593,7 +591,7 @@ class Correlator: self._build_integral_factor() def __call__(self, mu=0, temperature=0): """Returns the linear response χ_{α β}(µ, T) """Returns the linear response :math:χ_{α β}(µ, T) Parameters ---------- ... ...
 ... ... @@ -944,7 +944,7 @@ class magnetic_gauge: Parameters ---------- syst : kwant.builder.FiniteSystem or kwant.builder.InfiniteSystem syst : kwant.builder.FiniteSystem or kwant.builder.InfiniteSystem Examples -------- ... ... @@ -1027,7 +1027,7 @@ class magnetic_gauge: The first callable computes the Peierls phase in the scattering region and the remaining callables compute the Peierls phases in each of the leads. Each callable takes a pair of ~kwant.builder.Sites 'a, b' and returns a unit complex ~kwant.builder.Site (a hopping) and returns a unit complex number (Peierls phase) that multiplies that hopping. """ return self._peierls(syst_field, *lead_fields, tol=tol, average=False)
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!