doc/source/images/_defs.py

-################################################################
-# Make matplotlib work without X11
-################################################################
-import matplotlib
-matplotlib.use('Agg')
-
-################################################################
-# Prepend Kwant's build directory to sys.path
-################################################################
-import sys
-from distutils.util import get_platform
-sys.path.insert(0, "../../../build/lib.{0}-{1}.{2}".format(
-        get_platform(), *sys.version_info[:2]))
-
-################################################################
-# Define constants for plotting
-################################################################
-pt_to_in = 1. / 72.
-
-# Default width of figures in pts
-figwidth_pt = 600
-figwidth_in = figwidth_pt * pt_to_in
-
-# Width for smaller figures
-figwidth_small_pt = 400
-figwidth_small_in = figwidth_small_pt * pt_to_in
-
-# Sizes for matplotlib figures
-mpl_width_in = figwidth_pt * pt_to_in
-mpl_label_size = None  # font sizes in points
-mpl_tick_size = None
-
-# dpi for conversion from inches
-dpi = 90

doc/source/images/ab_ring.py.diff

---- original
-+++ modified
-@@ -12,6 +12,7 @@
- #    example, but in the tutorial main text)
- #  - Modifcations of hoppings/sites after they have been added
- 
-+import _defs
- from cmath import exp
- from math import pi
- 
-@@ -81,6 +82,50 @@
-     return syst
- 
- 
-+def make_system_note1(a=1, t=1.0, W=10, r1=10, r2=20):
-+    lat = kwant.lattice.square(a)
-+    syst = kwant.Builder()
-+    def ring(pos):
-+        (x, y) = pos
-+        rsq = x**2 + y**2
-+        return ( r1**2 < rsq < r2**2)
-+    syst[lat.shape(ring, (0, 11))] = 4 * t
-+    syst[lat.neighbors()] = -t
-+    sym_lead0 = kwant.TranslationalSymmetry((-a, 0))
-+    lead0 = kwant.Builder(sym_lead0)
-+    def lead_shape(pos):
-+        (x, y) = pos
-+        return (-1 < x < 1) and ( 0.5 * W < y < 1.5 * W )
-+    lead0[lat.shape(lead_shape, (0, W))] = 4 * t
-+    lead0[lat.neighbors()] = -t
-+    lead1 = lead0.reversed()
-+    syst.attach_lead(lead0)
-+    syst.attach_lead(lead1)
-+    return syst
-+
-+
-+def make_system_note2(a=1, t=1.0, W=10, r1=10, r2=20):
-+    lat = kwant.lattice.square(a)
-+    syst = kwant.Builder()
-+    def ring(pos):
-+        (x, y) = pos
-+        rsq = x**2 + y**2
-+        return ( r1**2 < rsq < r2**2)
-+    syst[lat.shape(ring, (0, 11))] = 4 * t
-+    syst[lat.neighbors()] = -t
-+    sym_lead0 = kwant.TranslationalSymmetry((-a, 0))
-+    lead0 = kwant.Builder(sym_lead0)
-+    def lead_shape(pos):
-+        (x, y) = pos
-+        return (-1 < x < 1) and ( -W/2 < y < W/2  )
-+    lead0[lat.shape(lead_shape, (0, 0))] = 4 * t
-+    lead0[lat.neighbors()] = -t
-+    lead1 = lead0.reversed()
-+    syst.attach_lead(lead0)
-+    syst.attach_lead(lead1, lat(0, 0))
-+    return syst
-+
-+
- def plot_conductance(syst, energy, fluxes):
-     # compute conductance
- 
-@@ -90,18 +135,31 @@
-         smatrix = kwant.smatrix(syst, energy, args=[flux])
-         data.append(smatrix.transmission(1, 0))
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(normalized_fluxes, data)
--    pyplot.xlabel("flux [flux quantum]")
--    pyplot.ylabel("conductance [e^2/h]")
--    pyplot.show()
-+    pyplot.xlabel("flux [flux quantum]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("conductance [e^2/h]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    fig.savefig("ab_ring_result.pdf")
-+    fig.savefig("ab_ring_result.png", dpi=_defs.dpi)
- 
- 
- def main():
-     syst = make_system()
- 
-     # Check that the system looks as intended.
--    kwant.plot(syst)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(syst, file="ab_ring_syst." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
-+
- 
-     # Finalize the system.
-     syst = syst.finalized()
-@@ -111,6 +169,17 @@
-                                                 for i in range(100)])
- 
- 
-+    # Finally, some plots needed for the notes
-+    syst = make_system_note1()
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(syst, file="ab_ring_note1." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
-+    syst = make_system_note2()
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(syst, file="ab_ring_note2." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
-+
-+
- # Call the main function if the script gets executed (as opposed to imported).
- # See <http://docs.python.org/library/__main__.html>.
- if __name__ == '__main__':

doc/source/images/band_structure.py.diff

---- original
-+++ modified
-@@ -9,6 +9,7 @@
- # --------------------------
- #  - Computing the band structure of a finalized lead.
- 
-+import _defs
- import kwant
- 
- # For plotting.
-@@ -36,10 +37,19 @@
- 
- def main():
-     lead = make_lead().finalized()
--    kwant.plotter.bands(lead, show=False)
--    pyplot.xlabel("momentum [(lattice constant)^-1]")
--    pyplot.ylabel("energy [t]")
--    pyplot.show()
-+    fig = kwant.plotter.bands(lead, show=False)
-+    pyplot.xlabel("momentum [(lattice constant)^-1]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("energy [t]", fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("band_structure_result." + extension, dpi=_defs.dpi)
-+
- 
- 
- # Call the main function if the script gets executed (as opposed to imported).

doc/source/images/closed_system.py.diff

---- original
-+++ modified
-@@ -11,6 +11,7 @@
- #  - Use of `hamiltonian_submatrix` in order to obtain a Hamiltonian
- #    matrix.
- 
-+import _defs
- from cmath import exp
- import numpy as np
- import kwant
-@@ -68,24 +69,39 @@
- 
-         energies.append(ev)
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(Bfields, energies)
--    pyplot.xlabel("magnetic field [arbitrary units]")
--    pyplot.ylabel("energy [t]")
--    pyplot.show()
-+    pyplot.xlabel("magnetic field [arbitrary units]",
-+                  fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("energy [t]", fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+                fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+                fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("closed_system_result." + extension, dpi=_defs.dpi)
- 
- 
- def plot_wave_function(syst):
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+
-     # Calculate the wave functions in the system.
-     ham_mat = syst.hamiltonian_submatrix(sparse=True)
-     evecs = sla.eigsh(ham_mat, k=20, which='SM')[1]
- 
-     # Plot the probability density of the 10th eigenmode.
--    kwant.plotter.map(syst, np.abs(evecs[:, 9])**2,
--                      colorbar=False, oversampling=1)
-+    for extension in ('pdf', 'png'):
-+        kwant.plotter.map(
-+            syst, np.abs(evecs[:, 9])**2, colorbar=False, oversampling=1,
-+            file="closed_system_eigenvector." + extension,
-+            fig_size=size, dpi=_defs.dpi)
- 
- 
- def plot_current(syst):
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+
-     # Calculate the wave functions in the system.
-     ham_mat = syst.hamiltonian_submatrix(sparse=True)
-     evecs = sla.eigsh(ham_mat, k=20, which='SM')[1]
-@@ -93,15 +109,16 @@
-     # Calculate and plot the local current of the 10th eigenmode.
-     J = kwant.operator.Current(syst)
-     current = J(evecs[:, 9])
--    kwant.plotter.current(syst, current, colorbar=False)
-+    for extension in ('pdf', 'png'):
-+        kwant.plotter.current(
-+            syst, current, colorbar=False,
-+            file="closed_system_current." + extension,
-+            fig_size=size, dpi=_defs.dpi)
- 
- 
- def main():
-     syst = make_system()
- 
--    # Check that the system looks as intended.
--    kwant.plot(syst)
--
-     # Finalize the system.
-     syst = syst.finalized()
- 

doc/source/images/discretize.py.diff

---- original
-+++ modified
-@@ -9,6 +9,7 @@
- # --------------------------
- #  - kwant.continuum.discretize
- 
-+import _defs
- 
- import kwant
- import scipy.sparse.linalg
-@@ -20,10 +21,19 @@
- from matplotlib import pyplot as plt
- 
- 
-+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')
-+
-+
- def stadium_system(L=20, W=20):
-     hamiltonian = "k_x**2 + k_y**2 + V(x, y)"
-     template = kwant.continuum.discretize(hamiltonian)
--    print(template)
-+    with open('discretizer_verbose.txt', 'w') as f:
-+        print(template, file=f)
- 
-     def stadium(site):
-         (x, y) = site.pos
-@@ -44,7 +54,7 @@
-     ham = syst.hamiltonian_submatrix(params=dict(V=potential), sparse=True)
-     evecs = scipy.sparse.linalg.eigsh(ham, k=10, which='SM')[1]
-     kwant.plotter.map(syst, abs(evecs[:, n])**2, show=False)
--    plt.show()
-+    save_figure('discretizer_gs')
- 
- 
- def qsh_system(a=20, L=2000, W=1000):
-@@ -91,7 +101,8 @@
-     plt.ylim(-0.05, 0.05)
-     plt.xlabel('momentum [1/A]')
-     plt.ylabel('energy [eV]')
--    plt.show()
-+    save_figure('discretizer_qsh_band')
-+
-     # get scattering wave functions at E=0
-     wf = kwant.wave_function(syst, energy=0, params=params)
- 
-@@ -119,7 +130,7 @@
- 
-     ax1.set_title('Probability density')
-     ax2.set_title('Spin density')
--    plt.show()
-+    save_figure('discretizer_qsh_wf')
- 
- 
- def lattice_spacing():
-@@ -160,7 +171,7 @@
- 
-     plot(ax1, a=1)
-     plot(ax2, a=.25)
--    plt.show()
-+    save_figure('discretizer_lattice_spacing')
- 
- 
- def substitutions():
-@@ -173,15 +184,18 @@
-         sympify('k_x**2 * sz + alpha * k_x * sx', locals=subs),
-     )
- 
--    print(e[0] == e[1] == e[2])
-+    with open('discretizer_subs_1.txt', 'w') as f:
-+        print(e[0] == e[1] == e[2], file=f)
- 
-     subs = {'A': 'A(x) + B', 'V': 'V(x) + V_0', 'C': 5}
--    print(sympify('k_x * A * k_x + V + C', locals=subs))
-+    with open('discretizer_subs_2.txt', 'w') as f:
-+        print(sympify('k_x * A * k_x + V + C', locals=subs), file=f)
- 
- 
- def main():
-     template = kwant.continuum.discretize('k_x * A(x) * k_x')
--    print(template)
-+    with open('discretizer_intro_verbose.txt', 'w') as f:
-+        print(template, file=f)
- 
-     syst = stadium_system()
-     plot_eigenstate(syst)

doc/source/images/generate-diffs.sh

-# !/bin/sh
-
-# This script regenerates the .diff files in this directory.  It's these files
-# that are kept under vesion control instead of the scripts themselves.
-
-for f in [a-zA-Z]*.py; do
-    # We use custom labels to suppress the time stamps which are unnecessary
-    # here and would only lead to noise in version control.
-    grep -v '#HIDDEN' ../tutorial/$f |
-    diff -u --label original --label modified - $f >$f.diff_
-    if cmp $f.diff_ $f.diff >/dev/null 2>&1; then
-        rm $f.diff_
-    else
-        mv $f.diff_ $f.diff
-    fi
-done

doc/source/images/graphene.py.diff

---- original
-+++ modified
-@@ -10,6 +10,7 @@
- #  - Application of all the aspects of tutorials 1-3 to a more complicated
- #    lattice, namely graphene
- 
-+import _defs
- from math import pi, sqrt, tanh
- 
- import kwant
-@@ -96,22 +97,40 @@
-         smatrix = kwant.smatrix(syst, energy)
-         data.append(smatrix.transmission(0, 1))
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(energies, data)
--    pyplot.xlabel("energy [t]")
--    pyplot.ylabel("conductance [e^2/h]")
--    pyplot.show()
-+    pyplot.xlabel("energy [t]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("conductance [e^2/h]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("graphene_result." + extension, dpi=_defs.dpi)
- 
- 
- def plot_bandstructure(flead, momenta):
-     bands = kwant.physics.Bands(flead)
-     energies = [bands(k) for k in momenta]
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(momenta, energies)
--    pyplot.xlabel("momentum [(lattice constant)^-1]")
--    pyplot.ylabel("energy [t]")
--    pyplot.show()
-+    pyplot.xlabel("momentum [(lattice constant)^-1]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("energy [t]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("graphene_bs." + extension, dpi=_defs.dpi)
- 
- 
- def main():
-@@ -123,8 +142,11 @@
-     def family_colors(site):
-         return 0 if site.family == a else 1
- 
--    # Plot the closed system without leads.
--    kwant.plot(syst, site_color=family_colors, site_lw=0.1, colorbar=False)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(syst, site_color=family_colors, site_lw=0.1, colorbar=False,
-+                   file="graphene_syst1." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
-     # Compute some eigenvalues.
-     compute_evs(syst.finalized())
-@@ -133,9 +155,11 @@
-     for lead in leads:
-         syst.attach_lead(lead)
- 
--    # Then, plot the system with leads.
--    kwant.plot(syst, site_color=family_colors, site_lw=0.1,
--               lead_site_lw=0, colorbar=False)
-+    size = (_defs.figwidth_in, 0.9 * _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(syst, site_color=family_colors, colorbar=False, site_lw=0.1,
-+                   file="graphene_syst2." + extension,
-+                   fig_size=size, dpi=_defs.dpi, lead_site_lw=0)
- 
-     # Finalize the system.
-     syst = syst.finalized()

doc/source/images/kernel_polynomial_method.py.diff

---- original
-+++ modified
-@@ -11,6 +11,9 @@
- 
- import scipy
- 
-+import _defs
-+from contextlib import redirect_stdout
-+
- # For plotting
- from matplotlib import pyplot as plt
- 
-@@ -36,13 +39,13 @@
- 
- 
- # Plot several density of states curves on the same axes.
--def plot_dos(labels_to_data):
-+def plot_dos(labels_to_data, file_name=None):
-     for label, (x, y) in labels_to_data:
-         plt.plot(x, y, label=label, linewidth=2)
-     plt.legend(loc=2, framealpha=0.5)
-     plt.xlabel("energy [t]")
-     plt.ylabel("DoS [a.u.]")
--    plt.show()
-+    save_figure(file_name)
-     plt.clf()
- 
- 
-@@ -57,10 +60,18 @@
-         kwant.plot(fsyst, site_size=site_size, site_color=(0, 0, 1, 0.3), ax=ax)
-         ax.set_title(title)
-         ax.set(adjustable='box-forced', aspect='equal')
--    plt.show()
-+    save_figure(file_name)
-     plt.clf()
- 
- 
-+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')
-+
-+
- def simple_dos_example():
-     fsyst = make_syst().finalized()
- 
-@@ -74,18 +85,24 @@
-     plot_dos([
-         ('densities', (energies, densities)),
-         ('density subset', (energy_subset, density_subset)),
--    ])
-+     ],
-+     file_name='kpm_dos'
-+    )
- 
- 
- def dos_integrating_example(fsyst):
-     spectrum = kwant.kpm.SpectralDensity(fsyst)
- 
--    print('identity resolution:', spectrum.integrate())
-+    with open('kpm_normalization.txt', 'w') as f:
-+        with redirect_stdout(f):
-+            print('identity resolution:', spectrum.integrate())
- 
-     # Fermi energy 0.1 and temperature 0.2
-     fermi = lambda E: 1 / (np.exp((E - 0.1) / 0.2) + 1)
- 
--    print('number of filled states:', spectrum.integrate(fermi))
-+    with open('kpm_total_states.txt', 'w') as f:
-+        with redirect_stdout(f):
-+            print('number of filled states:', spectrum.integrate(fermi))
- 
- 
- def increasing_accuracy_example(fsyst):
-@@ -99,7 +116,9 @@
-     plot_dos([
-         ('density', original_dos),
-         ('higher energy resolution', increased_resolution_dos),
--    ])
-+     ],
-+     file_name='kpm_dos_acc'
-+    )
- 
-     spectrum.add_moments(100)
-     spectrum.add_vectors(5)
-@@ -109,7 +128,9 @@
-     plot_dos([
-         ('density', original_dos),
-         ('higher number of moments', increased_moments_dos),
--    ])
-+     ],
-+     file_name='kpm_dos_r'
-+    )
- 
- 
- def operator_example(fsyst):
-@@ -139,7 +160,9 @@
-     plot_ldos(fsyst, axes,[
-         ('energy = 0', zero_energy_ldos),
-         ('energy = 1', finite_energy_ldos),
--    ])
-+     ],
-+     file_name='kpm_ldos'
-+    )
- 
- 
- def vector_factory_example(fsyst):

doc/source/images/magnetic_texture.py.diff

---- original
-+++ modified
-@@ -11,6 +11,9 @@
- #  - operators
- #  - plotting vector fields
- 
-+import _defs
-+from contextlib import redirect_stdout
-+
- from math import sin, cos, tanh, pi
- import itertools
- import numpy as np
-@@ -79,7 +82,13 @@
-     return syst
- 
- 
--def plot_vector_field(syst, params):
-+def save_plot(fname):
-+    for extension in ('.pdf', '.png'):
-+        plt.savefig(fname + extension,
-+                    dpi=_defs.dpi, bbox_inches='tight')
-+
-+
-+def plot_vector_field(syst, params, fname=None):
-     xmin, ymin = min(s.tag for s in syst.sites)
-     xmax, ymax = max(s.tag for s in syst.sites)
-     x, y = np.meshgrid(np.arange(xmin, xmax+1), np.arange(ymin, ymax+1))
-@@ -88,28 +97,38 @@
-     m_i = np.reshape(m_i, x.shape + (3,))
-     m_i = np.rollaxis(m_i, 2, 0)
- 
--    fig, ax = plt.subplots(1, 1)
-+    fig, ax = plt.subplots(1, 1, figsize=(9, 7))
-     im = ax.quiver(x, y, *m_i, pivot='mid', scale=75)
-     fig.colorbar(im)
--    plt.show()
-+    if fname:
-+        save_plot(fname)
-+    else:
-+        plt.show()
- 
- 
--def plot_densities(syst, densities):
--    fig, axes = plt.subplots(1, len(densities))
-+def plot_densities(syst, densities, fname=None):
-+    fig, axes = plt.subplots(1, len(densities), figsize=(7*len(densities), 7))
-     for ax, (title, rho) in zip(axes, densities):
-         kwant.plotter.map(syst, rho, ax=ax, a=4)
-         ax.set_title(title)
--    plt.show()
-+    if fname:
-+        save_plot(fname)
-+    else:
-+        plt.show()
-+
- 
- 
--def plot_currents(syst, currents):
--    fig, axes = plt.subplots(1, len(currents))
-+def plot_currents(syst, currents, fname=None):
-+    fig, axes = plt.subplots(1, len(currents), figsize=(7*len(currents), 7))
-     if not hasattr(axes, '__len__'):
-         axes = (axes,)
-     for ax, (title, current) in zip(axes, currents):
-         kwant.plotter.current(syst, current, ax=ax, colorbar=False)
-         ax.set_title(title)
--    plt.show()
-+    if fname:
-+        save_plot(fname)
-+    else:
-+        plt.show()
- 
- 
- def main():
-@@ -119,7 +138,7 @@
-     wf = kwant.wave_function(syst, energy=-1, params=params)
-     psi = wf(0)[0]
- 
--    plot_vector_field(syst, dict(r0=20, delta=10))
-+    plot_vector_field(syst, dict(r0=20, delta=10), fname='mag_field_direction')
- 
-     # even (odd) indices correspond to spin up (down)
-     up, down = psi[::2], psi[1::2]
-@@ -144,7 +163,7 @@
-         ('$σ_0$', density),
-         ('$σ_z$', spin_z),
-         ('$σ_y$', spin_y),
--    ])
-+    ], fname='spin_densities')
- 
-     J_0 = kwant.operator.Current(syst)
-     J_z = kwant.operator.Current(syst, sigma_z)
-@@ -159,7 +178,7 @@
-         ('$J_{σ_0}$', current),
-         ('$J_{σ_z}$', spin_z_current),
-         ('$J_{σ_y}$', spin_y_current),
--    ])
-+    ], fname='spin_currents')
- 
-     def following_m_i(site, r0, delta):
-         m_i = field_direction(site.pos, r0, delta)
-@@ -173,7 +192,7 @@
-     plot_currents(syst, [
-         (r'$J_{\mathbf{m}_i}$', m_current),
-         ('$J_{σ_z}$', spin_z_current),
--    ])
-+    ], fname='spin_current_comparison')
- 
- 
-     def circle(site):
-@@ -183,7 +202,9 @@
- 
-     all_states = np.vstack((wf(0), wf(1)))
-     dos_in_circle = sum(rho_circle(p) for p in all_states) / (2 * pi)
--    print('density of states in circle:', dos_in_circle)
-+    with open('circle_dos.txt', 'w') as f:
-+        with redirect_stdout(f):
-+            print('density of states in circle:', dos_in_circle)
- 
-     def left_cut(site_to, site_from):
-         return site_from.pos[0] <= -39 and site_to.pos[0] > -39
-@@ -197,8 +218,10 @@
-     Jz_left = kwant.operator.Current(syst, sigma_z, where=left_cut, sum=True)
-     Jz_right = kwant.operator.Current(syst, sigma_z, where=right_cut, sum=True)
- 
--    print('J_left:', J_left(psi), ' J_right:', J_right(psi))
--    print('Jz_left:', Jz_left(psi), ' Jz_right:', Jz_right(psi))
-+    with open('current_cut.txt', 'w') as f:
-+        with redirect_stdout(f):
-+            print('J_left:', J_left(psi), ' J_right:', J_right(psi))
-+            print('Jz_left:', Jz_left(psi), ' Jz_right:', Jz_right(psi))
- 
-     J_m = kwant.operator.Current(syst, following_m_i)
-     J_z = kwant.operator.Current(syst, sigma_z)
-@@ -214,7 +237,7 @@
-     plot_currents(syst, [
-         (r'$J_{\mathbf{m}_i}$ (from left)', J_m_left),
-         (r'$J_{σ_z}$ (from left)', J_z_left),
--    ])
-+    ], fname='bound_current')
- 
- 
- if __name__ == '__main__':

doc/source/images/plot_graphene.py.diff

---- original
-+++ modified
-@@ -9,6 +9,7 @@
- # --------------------------
- #  - demonstrate different ways of plotting
- 
-+import _defs
- import kwant
- from matplotlib import pyplot
- 
-@@ -22,7 +23,7 @@
-         return x**2 + y**2 < r**2
- 
-     syst = kwant.Builder()
--    syst[lat.shape(circle, (0, 0))] = 0
-+    syst[lat.shape(circle, (0,0))] = 0
-     syst[lat.neighbors()] = t
-     syst.eradicate_dangling()
-     if tp:
-@@ -32,9 +33,11 @@
- 
- 
- def plot_system(syst):
--    kwant.plot(syst)
--    # the standard plot is ok, but not very intelligible. One can do
--    # better by playing wioth colors and linewidths
-+    # standard plot - not very intelligible for this particular situation
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(syst, file="plot_graphene_syst1." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
-     # use color and linewidths to get a better plot
-     def family_color(site):
-@@ -43,7 +46,11 @@
-     def hopping_lw(site1, site2):
-         return 0.04 if site1.family == site2.family else 0.1
- 
--    kwant.plot(syst, site_lw=0.1, site_color=family_color, hop_lw=hopping_lw)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(syst, site_lw=0.1, site_color=family_color,
-+                   hop_lw=hopping_lw, file="plot_graphene_syst2." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
- 
- def plot_data(syst, n):
-@@ -58,7 +65,11 @@
-     # the usual - works great in general, looks just a bit crufty for
-     # small systems
- 
--    kwant.plotter.map(syst, wf, oversampling=10, cmap='gist_heat_r')
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plotter.map(syst, wf, oversampling=10, cmap='gist_heat_r',
-+                          file="plot_graphene_data1." + extension,
-+                          fig_size=size, dpi=_defs.dpi)
- 
-     # use two different sort of triangles to cleanly fill the space
-     def family_shape(i):
-@@ -68,15 +79,22 @@
-     def family_color(i):
-         return 'black' if syst.sites[i].family == a else 'white'
- 
--    kwant.plot(syst, site_color=wf, site_symbol=family_shape,
--               site_size=0.5, hop_lw=0, cmap='gist_heat_r')
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(syst, site_color=wf, site_symbol=family_shape,
-+                   site_size=0.5, hop_lw=0, cmap='gist_heat_r',
-+                   file="plot_graphene_data2." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
-     # plot by changing the symbols itself
-     def site_size(i):
-         return 3 * wf[i] / wf.max()
- 
--    kwant.plot(syst, site_size=site_size, site_color=(0, 0, 1, 0.3),
--               hop_lw=0.1)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(syst, site_size=site_size, site_color=(0,0,1,0.3),
-+                   hop_lw=0.1, file="plot_graphene_data3." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
- 
- def main():

doc/source/images/plot_qahe.py.diff

---- original
-+++ modified
-@@ -11,6 +11,7 @@
- # + Use of `kwant.operator` to compute local current
- # + Use of `kwant.plotter.current` to plot local current
- 
-+import _defs
- import math
- import matplotlib.pyplot
- import kwant
-@@ -60,7 +61,10 @@
-     psi = kwant.wave_function(syst, energy=params['m'], params=params)(0)
-     J = kwant.operator.Current(syst).bind(params=params)
-     current = sum(J(p) for p in psi)
--    kwant.plotter.current(syst, current)
-+    for extension in ('pdf', 'png'):
-+        kwant.plotter.current(syst, current,
-+                              file="plot_qahe_current." + extension,
-+                              dpi=_defs.dpi)
- 
- 
- if __name__ == '__main__':

doc/source/images/plot_zincblende.py.diff

---- original
-+++ modified
-@@ -9,6 +9,7 @@
- # --------------------------
- #  - demonstrate different ways of plotting in 3D
- 
-+import _defs
- import kwant
- from matplotlib import pyplot
- 
-@@ -33,7 +34,10 @@
-     # checking shapes:
-     syst = make_cuboid()
- 
--    kwant.plot(syst)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(syst, file="plot_zincblende_syst1." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
-     # visualize the crystal structure better for a very small system
-     syst = make_cuboid(a=1.5, b=1.5, c=1.5)
-@@ -41,8 +45,12 @@
-     def family_colors(site):
-         return 'r' if site.family == a else 'g'
- 
--    kwant.plot(syst, site_size=0.18, site_lw=0.01, hop_lw=0.05,
--               site_color=family_colors)
-+    size = (_defs.figwidth_in, _defs.figwidth_in)
-+    for extension in ('pdf', 'png'):
-+        kwant.plot(syst, site_size=0.18, site_lw=0.01, hop_lw=0.05,
-+                   site_color=family_colors,
-+                   file="plot_zincblende_syst2." + extension,
-+                   fig_size=size, dpi=_defs.dpi)
- 
- 
- # Call the main function if the script gets executed (as opposed to imported).

doc/source/images/quantum_well.py.diff

---- original
-+++ modified
-@@ -9,6 +9,7 @@
- # --------------------------
- #  - Functions as values in Builder
- 
-+import _defs
- import kwant
- 
- # For plotting
-@@ -55,19 +56,25 @@
-         smatrix = kwant.smatrix(syst, energy, args=[-welldepth])
-         data.append(smatrix.transmission(1, 0))
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(welldepths, data)
--    pyplot.xlabel("well depth [t]")
--    pyplot.ylabel("conductance [e^2/h]")
--    pyplot.show()
-+    pyplot.xlabel("well depth [t]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("conductance [e^2/h]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("quantum_well_result." + extension, dpi=_defs.dpi)
- 
- 
- def main():
-     syst = make_system()
- 
--    # Check that the system looks as intended.
--    kwant.plot(syst)
--
-     # Finalize the system.
-     syst = syst.finalized()
- 

doc/source/images/quantum_wire.py.diff

---- original
-+++ modified
-@@ -11,6 +11,7 @@
- #  - Making scattering region and leads
- #  - Using the simple sparse solver for computing Landauer conductance
- 
-+import _defs
- from matplotlib import pyplot
- import kwant
- 
-@@ -69,7 +70,10 @@
- syst.attach_lead(right_lead)
- 
- # Plot it, to make sure it's OK
--kwant.plot(syst)
-+size = (_defs.figwidth_in, 0.3 * _defs.figwidth_in)
-+for extension in ('pdf', 'png'):
-+    kwant.plot(syst, file="quantum_wire_syst." + extension,
-+               fig_size=size, dpi=_defs.dpi)
- 
- # Finalize the system
- syst = syst.finalized()
-@@ -90,8 +94,13 @@
- 
- # Use matplotlib to write output
- # We should see conductance steps
--pyplot.figure()
-+fig = pyplot.figure()
- pyplot.plot(energies, data)
--pyplot.xlabel("energy [t]")
--pyplot.ylabel("conductance [e^2/h]")
--pyplot.show()
-+pyplot.xlabel("energy [t]", fontsize=_defs.mpl_label_size)
-+pyplot.ylabel("conductance [e^2/h]", fontsize=_defs.mpl_label_size)
-+pyplot.setp(fig.get_axes()[0].get_xticklabels(), fontsize=_defs.mpl_tick_size)
-+pyplot.setp(fig.get_axes()[0].get_yticklabels(), fontsize=_defs.mpl_tick_size)
-+fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+for extension in ('pdf', 'png'):
-+    fig.savefig("quantum_wire_result." + extension, dpi=_defs.dpi)

doc/source/images/spin_orbit.py.diff

---- original
-+++ modified
-@@ -13,6 +13,7 @@
- # --------------------------
- #  - Numpy matrices as values in Builder
- 
-+import _defs
- import kwant
- 
- # For plotting
-@@ -70,19 +71,24 @@
-         smatrix = kwant.smatrix(syst, energy)
-         data.append(smatrix.transmission(1, 0))
- 
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(energies, data)
--    pyplot.xlabel("energy [t]")
--    pyplot.ylabel("conductance [e^2/h]")
--    pyplot.show()
-+    pyplot.xlabel("energy [t]", fontsize=_defs.mpl_label_size)
-+    pyplot.ylabel("conductance [e^2/h]",
-+                 fontsize=_defs.mpl_label_size)
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+               fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("spin_orbit_result." + extension, dpi=_defs.dpi)
- 
- 
- def main():
-     syst = make_system()
- 
--    # Check that the system looks as intended.
--    kwant.plot(syst)
--
-     # Finalize the system.
-     syst = syst.finalized()
- 

doc/source/images/superconductor.py.diff

---- original
-+++ modified
-@@ -11,6 +11,7 @@
- #   using conservation laws.
- # - Use of discrete symmetries to relate scattering states.
- 
-+import _defs
- import kwant
- 
- import tinyarray
-@@ -18,6 +19,7 @@
- 
- # For plotting
- from matplotlib import pyplot
-+from contextlib import redirect_stdout
- 
- tau_x = tinyarray.array([[0, 1], [1, 0]])
- tau_y = tinyarray.array([[0, -1j], [1j, 0]])
-@@ -74,11 +76,19 @@
-         data.append(smatrix.submatrix((0, 0), (0, 0)).shape[0] -
-                     smatrix.transmission((0, 0), (0, 0)) +
-                     smatrix.transmission((0, 1), (0, 0)))
--    pyplot.figure()
-+    fig = pyplot.figure()
-     pyplot.plot(energies, data)
-     pyplot.xlabel("energy [t]")
-     pyplot.ylabel("conductance [e^2/h]")
--    pyplot.show()
-+    pyplot.setp(fig.get_axes()[0].get_xticklabels(),
-+                fontsize=_defs.mpl_tick_size)
-+    pyplot.setp(fig.get_axes()[0].get_yticklabels(),
-+                fontsize=_defs.mpl_tick_size)
-+    fig.set_size_inches(_defs.mpl_width_in, _defs.mpl_width_in * 3. / 4.)
-+    fig.subplots_adjust(left=0.15, right=0.95, top=0.95, bottom=0.15)
-+    for extension in ('pdf', 'png'):
-+        fig.savefig("superconductor_transport_result." + extension,
-+                    dpi=_defs.dpi)
- 
- def check_PHS(syst):
-     # Scattering matrix
-@@ -103,14 +113,13 @@
- def main():
-     syst = make_system(W=10)
- 
--    # Check that the system looks as intended.
--    kwant.plot(syst)
--
-     # Finalize the system.
-     syst = syst.finalized()
- 
-     # Check particle-hole symmetry of the scattering matrix
--    check_PHS(syst)
-+    with open('check_PHS_out.txt', 'w') as f:
-+        with redirect_stdout(f):
-+            check_PHS(syst)
- 
-     # Compute and plot the conductance
-     plot_conductance(syst, energies=[0.002 * i for i in range(-10, 100)])

doc/source/pre/whatsnew/0.2.rst

@@ -21,7 +21,7 @@ New MUMPS-based solver
 ----------------------
 The code for sparse matrix solvers has been reorganized and a new solver has
 been added next to `kwant.solvers.sparse`: `kwant.solvers.mumps`.  The new
-solver uses the `MUMPS <http://graal.ens-lyon.fr/MUMPS/>`_ software package and
+solver uses the `MUMPS <https://graal.ens-lyon.fr/MUMPS/>`_ software package and
 is much (typically several times) faster than the UMFPACK-based old solver.
 In addition, MUMPS uses considerably less memory for a given system while at
 the same time it is able to take advantage of more than 2 GiB of RAM.

doc/source/pre/whatsnew/1.0.rst

@@ -3,8 +3,8 @@ What's new in Kwant 1.0
 
 This article explains the new features in Kwant 1.0 compared to Kwant 0.2.
 Kwant 1.0 was released on 9 September 2013.  Please consult the `full list of
-changes in Kwant <https://git.kwant-project.org/kwant/log/?h=v1.0.5>`_ for all
-the changes up to the most recent bugfix release.
+changes in Kwant <https://gitlab.kwant-project.org/kwant/kwant/-/commits/v1.0.5>`_
+for all the changes up to the most recent bugfix release.
 
 
 Lattice and shape improvements

doc/source/pre/whatsnew/1.1.rst

@@ -4,7 +4,7 @@ What's new in Kwant 1.1
 This article explains the user-visible changes in Kwant 1.1.0, released on 21
 October 2015.  See also the `full list of changes up to the most recent bugfix
 release of the 1.1 series
-<https://gitlab.kwant-project.org/kwant/kwant/compare/v1.1.0...latest-1.1>`_.
+<https://gitlab.kwant-project.org/kwant/kwant/-/compare/v1.1.0...latest-1.1>`_.
 
 Harmonize `~kwant.physics.Bands` with `~kwant.physics.modes`
 ------------------------------------------------------------

doc/source/pre/whatsnew/1.2.rst

@@ -4,7 +4,7 @@ What's new in Kwant 1.2
 This article explains the user-visible changes in Kwant 1.2.2, released on 9
 December 2015.  See also the `full list of changes up to the most recent bugfix
 release of the 1.2 series
-<https://gitlab.kwant-project.org/kwant/kwant/compare/v1.2.2...latest-1.2>`_.
+<https://gitlab.kwant-project.org/kwant/kwant/-/compare/v1.2.2...latest-1.2>`_.
 
 Kwant 1.2 is identical to Kwant 1.1 except that it has been updated to run on
 Python 3.4 and above.  Bugfix releases for the 1.1 and 1.2 series will mirror