From 3457034248d354ab7b43d6d94618948f92f52d81 Mon Sep 17 00:00:00 2001
From: guanjihuan <34735497+guanjihuan@users.noreply.github.com>
Date: Sat, 5 Jun 2021 15:12:12 +0800
Subject: [PATCH] update

---
 Tutorial/{test.py => 0_test.py}               |  4 +-
 .../{Wilson_loop.py => 10_Wilson_loop.py}     | 38 ++++++-------
 ...read_and_write.py => 11_read_and_write.py} | 38 ++++++-------
 Tutorial/12_download.py                       |  5 ++
 .../{Pauli_matrix.py => 1_Pauli_matrix.py}    | 10 ++--
 ...ize.py => 2_Hamiltonian_of_finite_size.py} |  8 +--
 ..._Fourier_transform_and_band_structures.py} | 36 ++++++-------
 ...phene.py => 4_bands_of_zigzag_graphene.py} | 22 ++++----
 ...states.py => 5_total_density_of_states.py} | 12 ++---
 ...states.py => 6_local_density_of_states.py} | 54 +++++++++----------
 Tutorial/{conductance.py => 7_conductance.py} | 14 ++---
 ...ering_matrix.py => 8_scattering_matrix.py} | 12 ++---
 .../{Chern_number.py => 9_Chern_number.py}    | 34 ++++++------
 13 files changed, 146 insertions(+), 141 deletions(-)
 rename Tutorial/{test.py => 0_test.py} (91%)
 mode change 100755 => 100644
 rename Tutorial/{Wilson_loop.py => 10_Wilson_loop.py} (96%)
 mode change 100755 => 100644
 rename Tutorial/{read_and_write.py => 11_read_and_write.py} (96%)
 mode change 100755 => 100644
 create mode 100644 Tutorial/12_download.py
 rename Tutorial/{Pauli_matrix.py => 1_Pauli_matrix.py} (97%)
 mode change 100755 => 100644
 rename Tutorial/{Hamiltonian_of_finite_size.py => 2_Hamiltonian_of_finite_size.py} (98%)
 mode change 100755 => 100644
 rename Tutorial/{Fourier_transform_and_band_structures.py => 3_Fourier_transform_and_band_structures.py} (98%)
 mode change 100755 => 100644
 rename Tutorial/{bands_of_zigzag_graphene.py => 4_bands_of_zigzag_graphene.py} (97%)
 mode change 100755 => 100644
 rename Tutorial/{total_density_of_states.py => 5_total_density_of_states.py} (98%)
 mode change 100755 => 100644
 rename Tutorial/{local_density_of_states.py => 6_local_density_of_states.py} (97%)
 mode change 100755 => 100644
 rename Tutorial/{conductance.py => 7_conductance.py} (97%)
 mode change 100755 => 100644
 rename Tutorial/{scattering_matrix.py => 8_scattering_matrix.py} (96%)
 mode change 100755 => 100644
 rename Tutorial/{Chern_number.py => 9_Chern_number.py} (97%)
 mode change 100755 => 100644

diff --git a/Tutorial/test.py b/Tutorial/0_test.py
old mode 100755
new mode 100644
similarity index 91%
rename from Tutorial/test.py
rename to Tutorial/0_test.py
index ffd0ebb..1d702a5
--- a/Tutorial/test.py
+++ b/Tutorial/0_test.py
@@ -1,3 +1,3 @@
-import gjh
-
+import gjh
+
 gjh.test()
\ No newline at end of file
diff --git a/Tutorial/Wilson_loop.py b/Tutorial/10_Wilson_loop.py
old mode 100755
new mode 100644
similarity index 96%
rename from Tutorial/Wilson_loop.py
rename to Tutorial/10_Wilson_loop.py
index f13eb8d..34dd76b
--- a/Tutorial/Wilson_loop.py
+++ b/Tutorial/10_Wilson_loop.py
@@ -1,20 +1,20 @@
-import gjh
-import numpy as np
-import cmath
-from math import *
-
-def hamiltonian_function(k): # SSH model
-    gamma = 0.5
-    lambda0 = 1
-    delta = 0
-    hamiltonian = np.zeros((2, 2), dtype=complex)
-    hamiltonian[0,0] = delta
-    hamiltonian[1,1] = -delta
-    hamiltonian[0,1] = gamma+lambda0*cmath.exp(-1j*k)
-    hamiltonian[1,0] = gamma+lambda0*cmath.exp(1j*k)
-    return hamiltonian
-
-wilson_loop_array = gjh.calculate_wilson_loop(hamiltonian_function)
-print('wilson loop =', wilson_loop_array)
-p = np.log(wilson_loop_array)/2/pi/1j
+import gjh
+import numpy as np
+import cmath
+from math import *
+
+def hamiltonian_function(k): # SSH model
+    gamma = 0.5
+    lambda0 = 1
+    delta = 0
+    hamiltonian = np.zeros((2, 2), dtype=complex)
+    hamiltonian[0,0] = delta
+    hamiltonian[1,1] = -delta
+    hamiltonian[0,1] = gamma+lambda0*cmath.exp(-1j*k)
+    hamiltonian[1,0] = gamma+lambda0*cmath.exp(1j*k)
+    return hamiltonian
+
+wilson_loop_array = gjh.calculate_wilson_loop(hamiltonian_function)
+print('wilson loop =', wilson_loop_array)
+p = np.log(wilson_loop_array)/2/pi/1j
 print('p =', p, '\n')
\ No newline at end of file
diff --git a/Tutorial/read_and_write.py b/Tutorial/11_read_and_write.py
old mode 100755
new mode 100644
similarity index 96%
rename from Tutorial/read_and_write.py
rename to Tutorial/11_read_and_write.py
index 1dad216..3d17d93
--- a/Tutorial/read_and_write.py
+++ b/Tutorial/11_read_and_write.py
@@ -1,20 +1,20 @@
-import gjh
-import numpy as np
-
-x = np.array([1, 2, 3])
-y = np.array([5, 6, 7])
-gjh.write_one_dimensional_data(x, y, filename='one_dimensional_data')
-
-matrix = np.zeros((3, 3))
-matrix[0, 1] = 11
-gjh.write_two_dimensional_data(x, y, matrix, filename='two_dimensional_data')
-
-
-x_read, y_read = gjh.read_one_dimensional_data('one_dimensional_data')
-print(x_read, '\n')
-print(y_read, '\n\n')
-
-x_read, y_read, matrix_read = gjh.read_two_dimensional_data('two_dimensional_data')
-print(x_read, '\n')
-print(y_read, '\n')
+import gjh
+import numpy as np
+
+x = np.array([1, 2, 3])
+y = np.array([5, 6, 7])
+gjh.write_one_dimensional_data(x, y, filename='one_dimensional_data')
+
+matrix = np.zeros((3, 3))
+matrix[0, 1] = 11
+gjh.write_two_dimensional_data(x, y, matrix, filename='two_dimensional_data')
+
+
+x_read, y_read = gjh.read_one_dimensional_data('one_dimensional_data')
+print(x_read, '\n')
+print(y_read, '\n\n')
+
+x_read, y_read, matrix_read = gjh.read_two_dimensional_data('two_dimensional_data')
+print(x_read, '\n')
+print(y_read, '\n')
 print(matrix_read)
\ No newline at end of file
diff --git a/Tutorial/12_download.py b/Tutorial/12_download.py
new file mode 100644
index 0000000..f6a62f0
--- /dev/null
+++ b/Tutorial/12_download.py
@@ -0,0 +1,5 @@
+import gjh
+
+gjh.download_with_scihub()
+# gjh.download_with_scihub('address')
+# gjh.download_with_scihub(num=3)
\ No newline at end of file
diff --git a/Tutorial/Pauli_matrix.py b/Tutorial/1_Pauli_matrix.py
old mode 100755
new mode 100644
similarity index 97%
rename from Tutorial/Pauli_matrix.py
rename to Tutorial/1_Pauli_matrix.py
index abe95ee..4403c0e
--- a/Tutorial/Pauli_matrix.py
+++ b/Tutorial/1_Pauli_matrix.py
@@ -1,6 +1,6 @@
-import gjh
-
-print('sigma_0:\n', gjh.sigma_0(), '\n')
-print('sigma_x:\n', gjh.sigma_x(), '\n')
-print('sigma_y:\n', gjh.sigma_y(), '\n')
+import gjh
+
+print('sigma_0:\n', gjh.sigma_0(), '\n')
+print('sigma_x:\n', gjh.sigma_x(), '\n')
+print('sigma_y:\n', gjh.sigma_y(), '\n')
 print('sigma_z:\n', gjh.sigma_z(), '\n')
\ No newline at end of file
diff --git a/Tutorial/Hamiltonian_of_finite_size.py b/Tutorial/2_Hamiltonian_of_finite_size.py
old mode 100755
new mode 100644
similarity index 98%
rename from Tutorial/Hamiltonian_of_finite_size.py
rename to Tutorial/2_Hamiltonian_of_finite_size.py
index 55aa9fb..aac1e0d
--- a/Tutorial/Hamiltonian_of_finite_size.py
+++ b/Tutorial/2_Hamiltonian_of_finite_size.py
@@ -1,5 +1,5 @@
-import gjh
-
-print(gjh.finite_size_along_one_direction(3), '\n')
-print(gjh.finite_size_along_two_directions_for_square_lattice(2, 2), '\n')
+import gjh
+
+print(gjh.finite_size_along_one_direction(3), '\n')
+print(gjh.finite_size_along_two_directions_for_square_lattice(2, 2), '\n')
 print(gjh.finite_size_along_three_directions_for_cubic_lattice(2, 2, 2), '\n')
\ No newline at end of file
diff --git a/Tutorial/Fourier_transform_and_band_structures.py b/Tutorial/3_Fourier_transform_and_band_structures.py
old mode 100755
new mode 100644
similarity index 98%
rename from Tutorial/Fourier_transform_and_band_structures.py
rename to Tutorial/3_Fourier_transform_and_band_structures.py
index 6c2cf95..3669a26
--- a/Tutorial/Fourier_transform_and_band_structures.py
+++ b/Tutorial/3_Fourier_transform_and_band_structures.py
@@ -1,19 +1,19 @@
-import gjh
-import numpy as np
-from math import *
-import functools
-
-x = np.linspace(-pi, pi, 100)
-y = np.linspace(-pi, pi, 100)
-
-hamiltonian_function = functools.partial(gjh.one_dimensional_fourier_transform, unit_cell=0, hopping=1)
-eigenvalue_array = gjh.calculate_eigenvalue_with_one_parameter(x, hamiltonian_function)
-gjh.plot(x, eigenvalue_array, xlabel='k', ylabel='E', type='-o')
-
-hamiltonian_function = functools.partial(gjh.two_dimensional_fourier_transform_for_square_lattice, unit_cell=0, hopping_1=1, hopping_2=1)
-eigenvalue_array = gjh.calculate_eigenvalue_with_two_parameters(x, y, hamiltonian_function)
-gjh.plot_3d_surface(x, y, eigenvalue_array, xlabel='kx', ylabel='ky', zlabel='E')
-
-hamiltonian_function = functools.partial(gjh.three_dimensional_fourier_transform_for_cubic_lattice, k3=0, unit_cell=0, hopping_1=1, hopping_2=1, hopping_3=1)
-eigenvalue_array = gjh.calculate_eigenvalue_with_two_parameters(x, y, hamiltonian_function)
+import gjh
+import numpy as np
+from math import *
+import functools
+
+x = np.linspace(-pi, pi, 100)
+y = np.linspace(-pi, pi, 100)
+
+hamiltonian_function = functools.partial(gjh.one_dimensional_fourier_transform, unit_cell=0, hopping=1)
+eigenvalue_array = gjh.calculate_eigenvalue_with_one_parameter(x, hamiltonian_function)
+gjh.plot(x, eigenvalue_array, xlabel='k', ylabel='E', type='-o')
+
+hamiltonian_function = functools.partial(gjh.two_dimensional_fourier_transform_for_square_lattice, unit_cell=0, hopping_1=1, hopping_2=1)
+eigenvalue_array = gjh.calculate_eigenvalue_with_two_parameters(x, y, hamiltonian_function)
+gjh.plot_3d_surface(x, y, eigenvalue_array, xlabel='kx', ylabel='ky', zlabel='E')
+
+hamiltonian_function = functools.partial(gjh.three_dimensional_fourier_transform_for_cubic_lattice, k3=0, unit_cell=0, hopping_1=1, hopping_2=1, hopping_3=1)
+eigenvalue_array = gjh.calculate_eigenvalue_with_two_parameters(x, y, hamiltonian_function)
 gjh.plot_3d_surface(x, y, eigenvalue_array, xlabel='kx', ylabel='ky', zlabel='E')
\ No newline at end of file
diff --git a/Tutorial/bands_of_zigzag_graphene.py b/Tutorial/4_bands_of_zigzag_graphene.py
old mode 100755
new mode 100644
similarity index 97%
rename from Tutorial/bands_of_zigzag_graphene.py
rename to Tutorial/4_bands_of_zigzag_graphene.py
index e70bf23..1a02233
--- a/Tutorial/bands_of_zigzag_graphene.py
+++ b/Tutorial/4_bands_of_zigzag_graphene.py
@@ -1,12 +1,12 @@
-import gjh
-import numpy as np
-from math import *
-import functools
-
-x = np.linspace(-pi, pi, 100)
-Ny = 10
-unit_cell = gjh.finite_size_along_two_directions_for_graphene(1, Ny)
-hopping = gjh.hopping_along_zigzag_direction_for_graphene(Ny)
-hamiltonian_function = functools.partial(gjh.one_dimensional_fourier_transform, unit_cell=unit_cell, hopping=hopping)
-eigenvalue_array = gjh.calculate_eigenvalue_with_one_parameter(x, hamiltonian_function)
+import gjh
+import numpy as np
+from math import *
+import functools
+
+x = np.linspace(-pi, pi, 100)
+Ny = 10
+unit_cell = gjh.finite_size_along_two_directions_for_graphene(1, Ny)
+hopping = gjh.hopping_along_zigzag_direction_for_graphene(Ny)
+hamiltonian_function = functools.partial(gjh.one_dimensional_fourier_transform, unit_cell=unit_cell, hopping=hopping)
+eigenvalue_array = gjh.calculate_eigenvalue_with_one_parameter(x, hamiltonian_function)
 gjh.plot(x, eigenvalue_array, xlabel='k', ylabel='E')
\ No newline at end of file
diff --git a/Tutorial/total_density_of_states.py b/Tutorial/5_total_density_of_states.py
old mode 100755
new mode 100644
similarity index 98%
rename from Tutorial/total_density_of_states.py
rename to Tutorial/5_total_density_of_states.py
index cd805c8..e2052b2
--- a/Tutorial/total_density_of_states.py
+++ b/Tutorial/5_total_density_of_states.py
@@ -1,7 +1,7 @@
-import gjh
-import numpy as np
-
-hamiltonian = gjh.finite_size_along_two_directions_for_square_lattice(2,2)
-fermi_energy_array = np.linspace(-4, 4, 400)
-total_dos_array = gjh.total_density_of_states_with_fermi_energy_array(fermi_energy_array, hamiltonian, broadening=0.1)
+import gjh
+import numpy as np
+
+hamiltonian = gjh.finite_size_along_two_directions_for_square_lattice(2,2)
+fermi_energy_array = np.linspace(-4, 4, 400)
+total_dos_array = gjh.total_density_of_states_with_fermi_energy_array(fermi_energy_array, hamiltonian, broadening=0.1)
 gjh.plot(fermi_energy_array, total_dos_array, xlabel='E', ylabel='Total DOS', type='-o')
\ No newline at end of file
diff --git a/Tutorial/local_density_of_states.py b/Tutorial/6_local_density_of_states.py
old mode 100755
new mode 100644
similarity index 97%
rename from Tutorial/local_density_of_states.py
rename to Tutorial/6_local_density_of_states.py
index 54920b6..1b284c8
--- a/Tutorial/local_density_of_states.py
+++ b/Tutorial/6_local_density_of_states.py
@@ -1,28 +1,28 @@
-import gjh
-import numpy as np
-
-fermi_energy = 0
-N1 = 3
-N2 = 4
-hamiltonian = gjh.finite_size_along_two_directions_for_square_lattice(N1,N2)
-LDOS = gjh.local_density_of_states_for_square_lattice(fermi_energy, hamiltonian, N1=N1, N2=N2)
-print('square lattice:\n', LDOS, '\n')
-
-h00 = gjh.finite_size_along_one_direction(N2)
-h01 = np.identity(N2)
-LDOS = gjh.local_density_of_states_for_square_lattice_using_dyson_equation(fermi_energy, h00=h00, h01=h01, N2=N2, N1=N1)
-print(LDOS, '\n\n')
-gjh.plot_contour(range(N1), range(N2), LDOS)
-
-
-N1 = 3
-N2 = 4
-N3 = 5
-hamiltonian = gjh.finite_size_along_three_directions_for_cubic_lattice(N1, N2, N3)
-LDOS = gjh.local_density_of_states_for_cubic_lattice(fermi_energy, hamiltonian, N1=N1, N2=N2, N3=N3)
-print('cubic lattice:\n', LDOS, '\n')
-
-h00 = gjh.finite_size_along_two_directions_for_square_lattice(N2, N3)
-h01 = np.identity(N2*N3)
-LDOS = gjh.local_density_of_states_for_cubic_lattice_using_dyson_equation(fermi_energy, h00, h01, N3=N3, N2=N2, N1=N1)
+import gjh
+import numpy as np
+
+fermi_energy = 0
+N1 = 3
+N2 = 4
+hamiltonian = gjh.finite_size_along_two_directions_for_square_lattice(N1,N2)
+LDOS = gjh.local_density_of_states_for_square_lattice(fermi_energy, hamiltonian, N1=N1, N2=N2)
+print('square lattice:\n', LDOS, '\n')
+
+h00 = gjh.finite_size_along_one_direction(N2)
+h01 = np.identity(N2)
+LDOS = gjh.local_density_of_states_for_square_lattice_using_dyson_equation(fermi_energy, h00=h00, h01=h01, N2=N2, N1=N1)
+print(LDOS, '\n\n')
+gjh.plot_contour(range(N1), range(N2), LDOS)
+
+
+N1 = 3
+N2 = 4
+N3 = 5
+hamiltonian = gjh.finite_size_along_three_directions_for_cubic_lattice(N1, N2, N3)
+LDOS = gjh.local_density_of_states_for_cubic_lattice(fermi_energy, hamiltonian, N1=N1, N2=N2, N3=N3)
+print('cubic lattice:\n', LDOS, '\n')
+
+h00 = gjh.finite_size_along_two_directions_for_square_lattice(N2, N3)
+h01 = np.identity(N2*N3)
+LDOS = gjh.local_density_of_states_for_cubic_lattice_using_dyson_equation(fermi_energy, h00, h01, N3=N3, N2=N2, N1=N1)
 print(LDOS)
\ No newline at end of file
diff --git a/Tutorial/conductance.py b/Tutorial/7_conductance.py
old mode 100755
new mode 100644
similarity index 97%
rename from Tutorial/conductance.py
rename to Tutorial/7_conductance.py
index 7cfa6de..10d5a94
--- a/Tutorial/conductance.py
+++ b/Tutorial/7_conductance.py
@@ -1,8 +1,8 @@
-import gjh
-import numpy as np
-
-fermi_energy_array = np.linspace(-5, 5, 400)
-h00 = gjh.finite_size_along_one_direction(4)
-h01 = np.identity(4)
-conductance_array = gjh.calculate_conductance_with_fermi_energy_array(fermi_energy_array, h00, h01)
+import gjh
+import numpy as np
+
+fermi_energy_array = np.linspace(-5, 5, 400)
+h00 = gjh.finite_size_along_one_direction(4)
+h01 = np.identity(4)
+conductance_array = gjh.calculate_conductance_with_fermi_energy_array(fermi_energy_array, h00, h01)
 gjh.plot(fermi_energy_array, conductance_array, xlabel='E', ylabel='Conductance', type='-o')
\ No newline at end of file
diff --git a/Tutorial/scattering_matrix.py b/Tutorial/8_scattering_matrix.py
old mode 100755
new mode 100644
similarity index 96%
rename from Tutorial/scattering_matrix.py
rename to Tutorial/8_scattering_matrix.py
index c84970d..c6a5f8e
--- a/Tutorial/scattering_matrix.py
+++ b/Tutorial/8_scattering_matrix.py
@@ -1,7 +1,7 @@
-import gjh
-import numpy as np
-
-fermi_energy = 0
-h00 = gjh.finite_size_along_one_direction(4)
-h01 = np.identity(4)
+import gjh
+import numpy as np
+
+fermi_energy = 0
+h00 = gjh.finite_size_along_one_direction(4)
+h01 = np.identity(4)
 gjh.print_or_write_scattering_matrix(fermi_energy, h00, h01)
\ No newline at end of file
diff --git a/Tutorial/Chern_number.py b/Tutorial/9_Chern_number.py
old mode 100755
new mode 100644
similarity index 97%
rename from Tutorial/Chern_number.py
rename to Tutorial/9_Chern_number.py
index 063738c..ef2d23a
--- a/Tutorial/Chern_number.py
+++ b/Tutorial/9_Chern_number.py
@@ -1,18 +1,18 @@
-import gjh
-import numpy as np
-from math import *
-
-def hamiltonian_function(kx, ky):  # one QAH model with chern number 2
-    t1 = 1.0
-    t2 = 1.0
-    t3 = 0.5
-    m = -1.0
-    hamiltonian = np.zeros((2, 2), dtype=complex)
-    hamiltonian[0, 1] = 2*t1*cos(kx)-1j*2*t1*cos(ky)
-    hamiltonian[1, 0] = 2*t1*cos(kx)+1j*2*t1*cos(ky)
-    hamiltonian[0, 0] = m+2*t3*sin(kx)+2*t3*sin(ky)+2*t2*cos(kx+ky)
-    hamiltonian[1, 1] = -(m+2*t3*sin(kx)+2*t3*sin(ky)+2*t2*cos(kx+ky))
-    return hamiltonian
-
-chern_number = gjh.calculate_chern_number_for_square_lattice(hamiltonian_function, precision=100)
+import gjh
+import numpy as np
+from math import *
+
+def hamiltonian_function(kx, ky):  # one QAH model with chern number 2
+    t1 = 1.0
+    t2 = 1.0
+    t3 = 0.5
+    m = -1.0
+    hamiltonian = np.zeros((2, 2), dtype=complex)
+    hamiltonian[0, 1] = 2*t1*cos(kx)-1j*2*t1*cos(ky)
+    hamiltonian[1, 0] = 2*t1*cos(kx)+1j*2*t1*cos(ky)
+    hamiltonian[0, 0] = m+2*t3*sin(kx)+2*t3*sin(ky)+2*t2*cos(kx+ky)
+    hamiltonian[1, 1] = -(m+2*t3*sin(kx)+2*t3*sin(ky)+2*t2*cos(kx+ky))
+    return hamiltonian
+
+chern_number = gjh.calculate_chern_number_for_square_lattice(hamiltonian_function, precision=100)
 print(chern_number)
\ No newline at end of file