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Commit 8fdc965a authored by Joseph Weston's avatar Joseph Weston
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clean up FAQ 

Apply pep8 fixes and refactor some sections to be more idiomatic
(e.g. avoiding triple nested loops). Also some minor reorganisation
of the sections to give the text a better flow.
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doc/source/images/FAQ.py.diff
+ 113
− 132
View file @ 8fdc965a
--- original
+++ modified
@@ -1,4 +1,4 @@
-
@@ -1,6 +1,7 @@
# Frequently Asked Questions
# ==========================
+import _defs
from cmath import exp
import numpy as np
import kwant
@@ -11,6 +11,13 @@
import numpy as np
import tinyarray
@@ -9,6 +10,12 @@
matplotlib.rcParams['figure.figsize'] = (3.5, 3.5)
######## What is a Site? ##############
+def save_figure(file_name):
+ if not file_name:
+ return
+ for extension in ('pdf', 'png'):
+ plt.savefig('.'.join((file_name,extension)),
+ plt.savefig('.'.join((file_name, extension)),
+ dpi=_defs.dpi, bbox_inches='tight')
+
+
######## What is a Site? ##############
a = 1
lat = kwant.lattice.square(a)
syst = kwant.Builder()
@@ -19,6 +26,7 @@
syst[lat(1,1)] = 4
syst[lat(1, 1)] = 4
kwant.plot(syst)
+save_figure('FAQ122')
+save_figure("FAQ122")
@@ -40,7 +48,14 @@
syst[lat2(0,0)] = 4 ## syst[subB(0,0)] = 4
@@ -40,6 +48,7 @@
syst[lat2(0, 0)] = 4 # syst[subB(0, 0)] = 4
kwant.plot(syst)
+save_figure('FAQ123')
+def save_figure(file_name):
+ if not file_name:
+ return
+ for extension in ('pdf', 'png'):
+ plt.savefig('.'.join((file_name,extension)),
+ dpi=_defs.dpi, bbox_inches='tight')
+save_figure("FAQ123")
########## What is a hopping? #######################
@@ -54,6 +69,7 @@
syst[(lat(1,0) , lat(1,1))] = -1
@@ -53,6 +62,7 @@
syst[(lat(1, 0), lat(1, 1))] = -1
kwant.plot(syst)
+save_figure('FAQ124')
+save_figure("FAQ124")
########### How to make a hole in a system? ###################"
@@ -73,7 +89,7 @@
@@ -69,6 +79,7 @@
syst[ (lat(i,j,k) for i in range(L) for j in range(W) for k in range(H)) ] = 4
syst[(lat(i, j, k) for i in range(L) for j in range(W) for k in range(H))] = 4
kwant.plot(syst)
-
+save_figure('FAQ1')
+save_figure("FAQ1")
## Deleting sites to create a hole
# Delete sites to create a hole
@@ -84,6 +100,7 @@
if ((L-2)*a/4 <= x <= 3*L*a/4) and (W*a/4 <= y <= 3*(W-2)*a/4) and (0 <= z <= (H-1)*a):
del syst[lat(i,j,k)]
kwant.plot(syst)
+save_figure('FAQ2')
@@ -80,6 +91,7 @@
del syst[site]
kwant.plot(syst)
+save_figure("FAQ2")
@@ -145,7 +162,7 @@
################ How can we get access to the sites of our system? ####################
@@ -133,7 +145,7 @@
## Plotting the system
plot_system(syst)
-
+save_figure('FAQ6B')
+save_figure("FAQ6B")
############### How to create every hoppings in a given direction using Hoppingkind? ################
@@ -149,6 +161,7 @@
@@ -162,7 +179,7 @@
syst[kwant.builder.HoppingKind((1,0), lat)] = -1
syst[kwant.builder.HoppingKind((1, 0), lat)] = -1
kwant.plot(syst)
-
+save_figure('FAQ3')
## Polyatomic lattice
+save_figure("FAQ3")
lat = kwant.lattice.kagome()
@@ -193,12 +210,13 @@
# Polyatomic lattice
syst[kwant.builder.HoppingKind((0,1), b, b)] = -1 # equivalent to syst[kwant.builder.HoppingKind((0,1), b)] = -1
@@ -181,12 +194,14 @@
# equivalent to syst[kwant.builder.HoppingKind((0, 1), b)] = -1
syst[kwant.builder.HoppingKind((0, 1), b, b)] = -1
plot_system(syst)
+save_figure('FAQ10')
del syst[kwant.builder.HoppingKind((0,1), b, b)] ## delete the hoppings previously created
syst[kwant.builder.HoppingKind((0,0), a, b)] = -1
syst[kwant.builder.HoppingKind((0,0), a, c)] = -1
syst[kwant.builder.HoppingKind((0,0), c, b)] = -1
+save_figure("FAQ10")
# Delete the hoppings previously created
del syst[kwant.builder.HoppingKind((0, 1), b, b)]
syst[kwant.builder.HoppingKind((0, 0), a, b)] = -1
syst[kwant.builder.HoppingKind((0, 0), a, c)] = -1
syst[kwant.builder.HoppingKind((0, 0), c, b)] = -1
plot_system(syst)
-
+save_figure('FAQ11')
+save_figure("FAQ11")
########## How to create the hoppings between adjacent sites? ################
@@ -213,11 +231,13 @@
@@ -201,11 +216,13 @@
syst[lat.neighbors()] = -1 ## equivalent to lat.neighbors(1)
syst[lat.neighbors()] = -1 # Equivalent to lat.neighbors(1)
kwant.plot(syst)
+save_figure('FAQ4')
+save_figure("FAQ4")
del syst[lat.neighbors()] ## deletes every hoppings previously created to add new one
del syst[lat.neighbors()] # Delete all nearest-neighbor hoppings
syst[lat.neighbors(2)] = -1
kwant.plot(syst)
+save_figure('FAQ5')
+save_figure("FAQ5")
## Polyatomic lattice
# Polyatomic lattice
@@ -224,14 +241,17 @@
@@ -236,14 +256,17 @@
## .neighbors()
syst[lat.neighbors()] = -1
plot_system(syst)
+save_figure('FAQ7')
del syst[lat.neighbors()] ## delete the hoppings previously created
+save_figure("FAQ7")
del syst[lat.neighbors()] # Delete the hoppings previously created
syst[a.neighbors()] = -1
plot_system(syst)
+save_figure('FAQ8')
del syst[a.neighbors()] ## deletes every hoppings previously created to add new one
+save_figure("FAQ8")
del syst[a.neighbors()] # Delete the hoppings previously created
syst[lat.neighbors(2)] = -1
plot_system(syst)
+save_figure('FAQ9')
+save_figure("FAQ9")
del syst[lat.neighbors(2)]
@@ -282,9 +305,10 @@
syst[ (subB(i,j) for i in range(L) for j in range(W)) ] = 4
@@ -264,6 +284,7 @@
syst[(subB(i, j) for i in range(L) for j in range(W))] = 4
syst[lat.neighbors()] = -1
plot_system(syst)
+save_figure('FAQAB')
## We manually add sites of the same lead lattice
-
+a = 2
lat2 = kwant.lattice.square(a)
def shapetop(pos):
@@ -303,6 +327,7 @@
syst[((lat2(i,-1), subA(i,0)) for i in range(5))] = -1
syst[((lat2(i+2,5), subB(i,4)) for i in range(5))] = -1
+save_figure("FAQAA")
# Create a lead
lat_lead = kwant.lattice.square()
@@ -273,6 +294,7 @@
lead1[(lat_lead(i, 0) for i in range(2, 7))] = 4
lead1[lat_lead.neighbors()] = -1
plot_system(lead1)
+save_figure("FAQAB")
syst[(lat_lead(i, 5) for i in range(2, 7))] = 4
syst[lat_lead.neighbors()] = -1
@@ -280,9 +302,11 @@
# Manually attach sites from graphene to square lattice
syst[((lat_lead(i+2, 5), subB(i, 4)) for i in range(5))] = -1
plot_system(syst)
+save_figure('FAQAC')
## Creation of the top lead
lat_lead = kwant.lattice.square(a)
@@ -320,6 +345,8 @@
+save_figure("FAQAC")
syst.attach_lead(lead1)
plot_system(syst)
+save_figure('FAQAD')
+
## Creation of the bottom lead
sym_lead2 = kwant.TranslationalSymmetry((0,-a))
@@ -335,6 +362,7 @@
syst.attach_lead(lead2)
plot_system(syst)
+save_figure('FAQAE')
+save_figure("FAQAD")
@@ -356,6 +384,7 @@
############# How to cut a finite system out of a system with translationnal symmetries? ###########
@@ -302,6 +326,7 @@
cuboid = kwant.Builder()
cuboid.fill(model, cuboid_shape, (0, 0, 0));
kwant.plot(cuboid);
+save_figure('FAQaaa')
+save_figure("FAQaaa")
# Build electrode (black).
def electrode_shape(site):
@@ -369,7 +398,7 @@
@@ -316,6 +341,7 @@
cuboid.attach_lead(electrode)
kwant.plot(cuboid);
-
+save_figure('FAQbbb')
+save_figure("FAQbbb")
###### How to extract the wavefunction informations on a specific site? ###############
@@ -389,6 +418,7 @@
syst.attach_lead(lead)
syst.attach_lead(lead.reversed())
kwant.plot(syst)
+save_figure('FAQBA')
fsyst = syst.finalized()
###### How does Kwant order the propagating modes of a lead? ######
@@ -348,6 +374,7 @@
plt.show()
@@ -401,6 +431,7 @@
plt.xlabel("momentum [(lattice constant)^-1]")
plt.ylabel("energy [t]")
plt.show()
+save_figure('FAQBB')
plot_and_label_modes(flead, E)
+save_figure('FAQPM')
plt.clf()
wf = kwant.wave_function(fsyst, Ef)
@@ -474,7 +505,7 @@
# More involved example
@@ -363,6 +390,7 @@
flead2 = lead2.finalized()
# Check that the system looks as intended.
kwant.plot(syst)
-
+save_figure('FAQTT')
# Finalize the system.
syst = syst.finalized()
@@ -488,7 +519,7 @@
plt.xlabel("momentum [(lattice constant)^-1]")
plt.ylabel("energy [t]")
plt.show()
-
+save_figure('FAQSS')
plot_and_label_modes(flead2, 1)
+save_figure('FAQPMC')
plt.clf()
wf = kwant.wave_function(syst, Ef)
@@ -395,7 +423,8 @@
idx = syst.id_by_site[lat(0, 0)] # look up index of site
-print('wavefunction on lat(0, 0): ', wf[idx])
+with open('FAQORD1.txt', 'w') as f:
+ print('wavefunction on lat(0, 0): ', wf[idx], file=f)
lat = kwant.lattice.square(norbs=2)
syst = make_system(lat)
@@ -408,4 +437,5 @@
# to degrees of freedom on the same site.
wf = wf.reshape(-1, 2)
-print('wavefunction on lat(0, 0): ', wf[idx])
+with open('FAQORD2.txt', 'w') as f:
+ print('wavefunction on lat(0, 0): ', wf[idx], file=f)
doc/source/tutorial/FAQ.py
+ 174
− 282
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doc/source/tutorial/FAQ.rst
+ 257
− 163
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