From c2cd6d1af48ad8aac399a60358582bea4c5ccb0d Mon Sep 17 00:00:00 2001
From: Joseph Weston <joseph@weston.cloud>
Date: Tue, 7 May 2019 14:18:27 +0200
Subject: [PATCH] add section to first_steps tutorial about script organization
---
doc/source/tutorial/first_steps.rst | 189 ++++++++++++++++++++--------
1 file changed, 139 insertions(+), 50 deletions(-)
diff --git a/doc/source/tutorial/first_steps.rst b/doc/source/tutorial/first_steps.rst
index 469cfbbb..bfb60e0c 100644
--- a/doc/source/tutorial/first_steps.rst
+++ b/doc/source/tutorial/first_steps.rst
@@ -13,7 +13,7 @@ Schrödinger equation
.. math::
H = \frac{-\hbar^2}{2m}(\partial_x^2 + \partial_y^2) + V(y)
-with a hard-wall confinement :math:`V(y)` in y-direction.
+with a hard-wall confinement :math:`V(y)` in the y-direction.
To be able to implement the quantum wire with Kwant, the continuous Hamiltonian
:math:`H` has to be discretized thus turning it into a tight-binding
@@ -94,7 +94,7 @@ In order to use Kwant, we need to import it:
Enabling Kwant is as easy as this [#]_ !
-The first step is now the definition of the system with scattering region and
+The first step is now to define the system with scattering region and
leads. For this we make use of the `~kwant.builder.Builder` type that allows to
define a system in a convenient way. We need to create an instance of it:
@@ -519,7 +519,7 @@ the right lead. The only difference was the direction of the translational
symmetry vector. Here, we only construct the left lead, and use the method
`~kwant.builder.Builder.reversed` of `~kwant.builder.Builder` to obtain a copy
of a lead pointing in the opposite direction. Both leads are attached as
-before and the finished system returned:
+before:
.. jupyter-execute::
:hide-output:
@@ -527,61 +527,29 @@ before and the finished system returned:
syst.attach_lead(lead)
syst.attach_lead(lead.reversed())
-
-The remainder of the script has been organized into two functions. One for the
-plotting of the conductance.
-
-
-.. jupyter-execute::
-
- def plot_conductance(syst, energies):
- # Compute conductance
- data = []
- for energy in energies:
- smatrix = kwant.smatrix(syst, energy)
- data.append(smatrix.transmission(1, 0))
-
- pyplot.figure()
- pyplot.plot(energies, data)
- pyplot.xlabel("energy [t]")
- pyplot.ylabel("conductance [e^2/h]")
- pyplot.show()
-
-And one ``main`` function.
+The remainder of the script proceeds identically. We first finalize the system:
.. jupyter-execute::
- def main():
- # Check that the system looks as intended.
- kwant.plot(syst)
-
- # Finalize the system.
- fsyst = syst.finalized()
-
- # We should see conductance steps.
- plot_conductance(fsyst, energies=[0.01 * i for i in range(100)])
-
-
-Finally, we use the following standard Python construct [#]_ to execute
-``main`` if the program is used as a script (i.e. executed as
-``python quantum_wire_revisited.py``):
+ syst = syst.finalized()
+and then calculate the transmission and plot:
.. jupyter-execute::
- # Call the main function if the script gets executed (as opposed to imported).
- # See <http://docs.python.org/library/__main__.html>.
- if __name__ == '__main__':
- main()
-
-
-If the example, however, is imported inside Python using ``import
-quantum_wire_revisted as qw``, ``main`` is not executed automatically.
-Instead, you can execute it manually using ``qw.main()``. On the other
-hand, you also have access to the other functions, ``make_system`` and
-``plot_conductance``, and can thus play with the parameters.
+ energies = []
+ data = []
+ for ie in range(100):
+ energy = ie * 0.01
+ smatrix = kwant.smatrix(syst, energy)
+ energies.append(energy)
+ data.append(smatrix.transmission(1, 0))
-The result of the example should be identical to the previous one.
+ pyplot.figure()
+ pyplot.plot(energies, data)
+ pyplot.xlabel("energy [t]")
+ pyplot.ylabel("conductance [e^2/h]")
+ pyplot.show()
.. specialnote:: Technical details
@@ -652,6 +620,127 @@ The result of the example should be identical to the previous one.
it would be impossible to distinguish whether one would like to add two
separate sites, or one hopping.
+
+Tips for organizing your simulation scripts
+...........................................
+
+.. seealso::
+ The complete source code of this example can be found in
+ :jupyter-download:script:`quantum_wire_organized`
+
+
+.. jupyter-kernel::
+ :id: quantum_wire_organized
+
+.. jupyter-execute::
+ :hide-code:
+
+ # Tutorial 2.2.4. Organizing a simulation script
+ # ==============================================
+ #
+ # Physics background
+ # ------------------
+ # Conductance of a quantum wire; subbands
+ #
+ # Note: Does the same as quantum_write_revisited.py, but features
+ # better code organization
+
+
+The above two examples illustrate some of the core features of Kwant, however
+the code was presented in a style which is good for exposition, but which is
+bad for making your code understandable and reusable. In this example we will
+lay out some best practices for writing your own simulation scripts.
+
+In the above examples we constructed a single Kwant system, using global variables
+for parameters such as the lattice constant and the length and width of the system.
+Instead, it is preferable to create a *function* that you can call, and which will
+return a Kwant ``Builder``:
+
+.. jupyter-execute::
+
+ from matplotlib import pyplot
+ import kwant
+
+ def make_system(L, W, a=1, t=1.0):
+ lat = kwant.lattice.square(a)
+
+ syst = kwant.Builder()
+ syst[(lat(i, j) for i in range(L) for j in range(W))] = 4 * t
+ syst[lat.neighbors()] = -t
+
+ lead = kwant.Builder(kwant.TranslationalSymmetry((-a, 0)))
+ lead[(lat(0, j) for j in range(W))] = 4 * t
+ lead[lat.neighbors()] = -t
+
+ syst.attach_lead(lead)
+ syst.attach_lead(lead.reversed())
+
+ return syst
+
+
+By encapsulating system creation within ``make_system`` we *document* our code
+by telling readers that *this* is how we create a system, and that creating a system
+depends on *these* parameters (the length and width of the system, in this case, as well
+as the lattice constant and the value for the hopping parameter). By defining a function
+we also ensure that we can consistently create different systems (e.g. of different sizes)
+of the same type (rectangular slab).
+
+We similarly encapsulate the part of the script that does computation and plotting into
+a function ``plot_conductance``:
+
+.. jupyter-execute::
+
+ def plot_conductance(syst, energies):
+ # Compute conductance
+ data = []
+ for energy in energies:
+ smatrix = kwant.smatrix(syst, energy)
+ data.append(smatrix.transmission(1, 0))
+
+ pyplot.figure()
+ pyplot.plot(energies, data)
+ pyplot.xlabel("energy [t]")
+ pyplot.ylabel("conductance [e^2/h]")
+ pyplot.show()
+
+And the ``main`` function that glues together the components that we previously defined:
+
+.. jupyter-execute::
+
+ def main():
+ syst = make_system(W=10, L=30)
+
+ # Check that the system looks as intended.
+ kwant.plot(syst)
+
+ # Finalize the system.
+ fsyst = syst.finalized()
+
+ # We should see conductance steps.
+ plot_conductance(fsyst, energies=[0.01 * i for i in range(100)])
+
+
+Finally, we use the following standard Python construct [#]_ to execute
+``main`` if the program is used as a script (i.e. executed as
+``python quantum_wire_organized.py``):
+
+
+.. jupyter-execute::
+
+ # Call the main function if the script gets executed (as opposed to imported).
+ # See <http://docs.python.org/library/__main__.html>.
+ if __name__ == '__main__':
+ main()
+
+If the example, however, is imported inside Python using ``import
+quantum_wire_organized as qw``, ``main`` is not executed automatically.
+Instead, you can execute it manually using ``qw.main()``. On the other
+hand, you also have access to the other functions, ``make_system`` and
+``plot_conductance``, and can thus play with the parameters.
+
+The result of this example should be identical to the previous one.
+
+
.. rubric:: Footnotes
.. [#] https://docs.python.org/3/library/__main__.html
--
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