.gitattributes

+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

.gitignore

@@ -4,4 +4,6 @@ site
 *.pyc
 __pycache__
 *.swp
-.cache
\ No newline at end of file
+.cache# pixi environments
+.pixi
+*.egg-info

.gitlab-ci.yml

-image: gitlab.kwant-project.org:5005/qt/research-docker
+variables:
+  FF_USE_FASTZIP: "true"
+  CACHE_COMPRESSION_LEVEL: "fastest"
 
 build lectures:
-  before_script:
-    - pip install -Ur requirements.txt
+  image: ghcr.io/prefix-dev/pixi:0.28.0
+  cache:
+    key: "$CI_JOB_NAME"
+    paths:
+        - .pixi
   script:
-    - PYDEVD_DISABLE_FILE_VALIDATION=1 mkdocs build
+    - pixi run build
   artifacts:
     paths:
       - site
@@ -12,6 +17,7 @@ build lectures:
   needs: []
 
 .prepare_deploy: &prepare_deploy
+  image: eeacms/rsync
   only:
     - branches@solidstate/lectures
   before_script:
@@ -31,10 +37,10 @@ build lectures:
     ## Create the SSH directory and give it the right permissions
     - mkdir -p ~/.ssh
     - chmod 700 ~/.ssh
-    - ssh-keyscan tnw-tn1.tudelft.net >> ~/.ssh/known_hosts
+    - ssh-keyscan qt4.tudelft.net >> ~/.ssh/known_hosts
     - chmod 644 ~/.ssh/known_hosts
   script:
-    - "rsync -rv site/* solidstate@tnw-tn1.tudelft.net:$DEPLOY_PATH"
+    - "rsync -rv site/* uploader@qt4.tudelft.net:$DEPLOY_PATH"
   needs:
     - build lectures
 
@@ -68,12 +74,13 @@ undeploy test version:
     DEPLOY_PATH: "test_builds/$CI_COMMIT_REF_NAME"
   script:
     - mkdir empty/
-    - "rsync -rlv --delete empty/ solidstate@tnw-tn1.tudelft.net:$DEPLOY_PATH"
+    - "rsync -rlv --delete empty/ uploader@qt4.tudelft.net:$DEPLOY_PATH"
   environment:
     name: $CI_COMMIT_REF_NAME
     action: stop
 
 merge into local:
+  image: bitnami/git
   only:
     - master@solidstate/lectures
   script:

docs/10_xray_solutions.md

@@ -76,9 +76,10 @@ The volume of the 1st Brillouin zone is the same as the volume of any other prim
 ## Exercise 3: X-ray scattering in 2D
 
 ```python
+b_y, b_x = 18.4, 13.4
 def reciprocal_lattice(N = 7, lim = 40):
-    y = np.repeat(np.linspace(-18.4*(N//2),18.4*(N//2),N),N)
-    x = np.tile(np.linspace(-13.4*(N//2),13.4*(N//2),N),N)
+    y = np.repeat(np.linspace(-b_y*(N//2),b_y*(N//2),N),N)
+    x = np.tile(np.linspace(-b_x*(N//2),b_x*(N//2),N),N)
 
     plt.figure(figsize=(5,5))
 
@@ -100,18 +101,20 @@ reciprocal_lattice()
 ```python
 reciprocal_lattice()
 # G vector
-plt.arrow(0,0,13.4*2,18.4,color='r',zorder=10,head_width=2,length_includes_head=True)
+plt.arrow(
+    b_x*2, b_y, -b_x*2, -b_y, color='r', zorder=10, head_width=2,length_includes_head=True,
+)
 plt.annotate('$\mathbf{G}$',(17,6.5),fontsize=14,ha='center',color='r')
 # k vector
 plt.arrow(-6,37.4,6,-37.4,color='b',zorder=11,head_width=2,length_includes_head=True)
 plt.annotate('$\mathbf{k}$',(-8,18),fontsize=14, ha='center',color='b')
 # k' vector
-plt.arrow(-6,37.4,6+13.4*2,-37.4+18.4,color='k',zorder=11,head_width=2,length_includes_head=True)
+plt.arrow(-6,37.4,6+b_x*2,-37.4+b_y,color='k',zorder=11,head_width=2,length_includes_head=True)
 plt.annotate('$\mathbf{k\'}$',(15,30),fontsize=14, ha='center',color='k');
 ```
 
 4.
-Since there is only 1 atom in the basis, there are no missing peaks due to a structure factor. We will get diffraction peaks at angles given by Bragg's law $\sin2\theta = \lambda/d_{hkl} = \lambda |\mathbf{G_{hkl}}|/2\pi$. We see that the shortest reciprocal lattice vector gives the smallest angle. Therefore, as a function of increasing $\theta$, we will see peaks at $(hkl)= (100) \quad (010) \quad (110) \quad (200), (020)$, where we took into account that $|\mathbf{b_1}|<|\mathbf{b_2}|$.
+Since there is only 1 atom in the basis, there are no missing peaks due to a structure factor. We will get diffraction peaks at angles given by Bragg's law $\sin2\theta = \lambda/d_{hkl} = \lambda |\mathbf{G_{hkl}}|/2\pi$. We see that the shortest reciprocal lattice vector gives the smallest angle. Therefore, as a function of increasing $\theta$, we will see peaks at $(hkl)= (10) \quad (01) \quad (11) \quad (20) \quad  (21) \quad (02)$, where we took into account that $|\mathbf{b_1}|<|\mathbf{b_2}|$.
 
 ## Exercise 4: Analyzing a 3D power diffraction spectrum
 

docs/11_nearly_free_electron_model_solutions.md

@@ -100,7 +100,7 @@ dispersions(5)
 First the kinetic term,
 
 \begin{equation*}
-\left\langle\phi_m|\hat{K}|\phi_n\right\rangle=C_m\frac{\hbar^2k_m^2}{2m}
+\left\langle\phi_m|\hat{K}|\psi\right\rangle=C_m\frac{\hbar^2k_m^2}{2m}
 \end{equation*}
 
 And the potential term,

docs/12_band_structures_in_higher_dimensions_solutions.md

@@ -86,12 +86,15 @@ Four in total: $(\pm\pi/a,\pm\pi/a)$.
 ### Question 3.
 
 Define a basis, e.g.
-\begin{align*}
-    \left|0\right\rangle &= (\pi/a,\pi/a) \\
-    \left|1\right\rangle &= (\pi/a,-\pi/a) \\
-    \left|2\right\rangle &= (-\pi/a,-\pi/a) \\
-    \left|3\right\rangle &= (-\pi/a,\pi/a)
-\end{align*}
+\begin{equation*}
+    \begin{align*}
+        \left|0\right\rangle &= (\pi/a,\pi/a) \\
+        \left|1\right\rangle &= (\pi/a,-\pi/a) \\
+        \left|2\right\rangle &= (-\pi/a,-\pi/a) \\
+        \left|3\right\rangle &= (-\pi/a,\pi/a)
+    \end{align*}
+\end{equation*}
+
 The Hamiltonian becomes
 
 $$

docs/13_semiconductors.md

@@ -264,7 +264,7 @@ Therefore, the fourth step assumes that the Fermi level is far from both bands $
 As a result, the Fermi-Dirac distribution is approximately similar to Boltzmann distribution:
 
 $$
-f(E)_{e/h} \approx \exp\left[-(E_{e/h}\pm E_F)/k_BT\right].
+f(E)_{e/h} \approx \exp\left[(-E_{e/h}\pm E_F)/k_BT\right].
 $$
 
 Now we can move to the last step and calculate $n_e$ and $n_h$:

docs/13_semiconductors_solutions.md

@@ -108,7 +108,7 @@ n_h \approx \int_{-E_v}^\infty\frac{m_h}{\pi\hbar^2}e^{-(E_h+E_F)/k_BT}dE_h = N_
 $$
 
 $$
-n_e \approx \int_{E_c}^\infty\frac{m_e}{\pi\hbar^2}e^{-(E-E_F)/k_BT}dE = N_C e^{-(E_c+E_F)/k_BT}
+n_e \approx \int_{E_c}^\infty\frac{m_e}{\pi\hbar^2}e^{-(E-E_F)/k_BT}dE = N_C e^{-(E_c-E_F)/k_BT}
 $$
 
 where
@@ -201,7 +201,7 @@ v_{vb,h} = -\frac{2at_{vb}}{\hbar}\sin (ka)
 $$
 
 $$
-m_{vb,h} =  -\frac{\hbar^2}{2a^2t_{vb}\cos (ka)}.
+m_{vb,h} =  \frac{\hbar^2}{2a^2t_{vb}\cos (ka)}.
 $$
 
 #### Question 2.

docs/14_doping_and_devices_solutions.md

@@ -107,7 +107,7 @@ This a "particle in a box" problem.
 
 \begin{align*}
 -\frac{\hbar^2}{2m_e^{\ast}} \nabla^2 \Psi_e &= (E_e-E_c)\Psi_e\\
--\frac{\hbar^2}{2m_h^{\ast}} \nabla^2 \Psi_h &= (-E_h-E_v)\Psi_h 
+-\frac{\hbar^2}{2m_h^{\ast}} \nabla^2 \Psi_h &= (E_h+E_v)\Psi_h 
 \end{align*}
 
 Here and below $E_h$ is the energy of a hole in the valence band.
@@ -116,7 +116,7 @@ Here and below $E_h$ is the energy of a hole in the valence band.
 
 \begin{align*}
 E_e = E_c + \frac{\hbar^2}{2m_e^{\ast}} ((\frac{\pi n}{L})^2+k_x^2+k_y^2),\\
--E_h = E_v - \frac{\hbar^2}{2m_h^{\ast}} ((\frac{\pi n}{L})^2+k_x^2+k_y^2)
+E_h = -E_v + \frac{\hbar^2}{2m_h^{\ast}} ((\frac{\pi n}{L})^2+k_x^2+k_y^2)
 \end{align*}
 
 ### Question 4.
@@ -131,7 +131,7 @@ g_h = \frac{m_h^{\ast}}{\pi\hbar^2}
 $L$ can be found here using previous questions, by setting:
 
 $$
-E_e - E_h - E_c + E_v = 1 eV = \frac{\hbar^2}{2}(\frac{\pi n}{L}^2+k_x^2+k_y^2)
+E_e + E_h - E_c + E_v = 1 eV = \frac{\hbar^2}{2}(\frac{\pi n}{L}^2+k_x^2+k_y^2)
 (\frac{1}{m_e^{\ast}}+\frac{1}{m_h^{\ast}})
 $$
 

docs/1_einstein_model.md

@@ -21,7 +21,6 @@ from scipy.optimize import curve_fit
 from scipy.integrate import quad
 import plotly.offline as py
 import plotly.graph_objs as go
-from ipywidgets import interact, FloatSlider, Layout
 
 from common import draw_classic_axes, configure_plotting
 

docs/6_bonds_and_spectra.md

@@ -2,7 +2,7 @@
 from matplotlib import pyplot
 from matplotlib.patches import Circle
 import numpy as np
-from scipy.integrate import simps
+from scipy.integrate import simpson
 
 from common import draw_classic_axes, configure_plotting
 import plotly.graph_objs as go
@@ -165,8 +165,8 @@ def line(E_t):
     return [left, right]
 
 def avg_pos_cubic(E_t):
-    Z = simps(np.exp(- U_cubic / E_t), r)
-    r_avg = simps(r * np.exp(- U_cubic / E_t), r)
+    Z = simpson(np.exp(- U_cubic / E_t), x=r)
+    r_avg = simpson(r * np.exp(- U_cubic / E_t), x=r)
     x = r_avg / Z
     return x
 

docs/7_tight_binding.md

@@ -379,7 +379,7 @@ The process of calculating the DOS at a given energy $E$ of a spin-independent H
 2. Compute $\rvert dk / dE \rvert$. Do this either by writing $k$ as a (multi-valued) function of $E$ and differentiating, or by computing $(dE / dk)^{-1}$.
 3. Sum or integrate $dk / dE$ over the allowed values of $k$ found in 1 and multiply by any degeneracies (spin/polarization).
 
-If the Hamiltonian depends on spin, then there is no spin degeneracy and the spin number $s$ must be treated in the same way as $k$.
+If the Hamiltonian depends on spin or polarization, then there are more branches of the dispersion relation, but each contains fewer states.
 
 ## Summary
 

docs/8_many_atoms_solutions.md

@@ -23,7 +23,7 @@ pi = np.pi
 
 2. Values of $k$ that differ by an integer multiple of $2\pi/a$ describe the same wave. Therefore, all information is already contained in the 1st Brillouin zone.
 
-3. The LCAO wavefunction is $|\Psi\rangle = \sum_n\phi_n|n\rangle$. The Schroedinger equation yields $\varepsilon \phi_n = \varepsilon_0 \phi_n - t \phi_{n+1} - t \phi_{n-1}$. Plugging in the Ansatz $\phi_n = \phi_0 e^{ikna}$ yields
+3. The LCAO wavefunction is $|\Psi\rangle = \sum_n\phi_n|n\rangle$. The Schrödinger equation yields $\varepsilon \phi_n = \varepsilon_0 \phi_n - t \phi_{n+1} - t \phi_{n-1}$. Plugging in the Ansatz $\phi_n = \phi_0 e^{ikna}$ yields
 $$
 \varepsilon = \varepsilon_0 -2t\cos(ka)
 $$

execute.py

-from pathlib import Path
-from logging import getLogger
-
-from mkdocs.structure.files import File
-from mkdocs.plugins import BasePlugin
-import nbconvert
-from nbconvert.preprocessors import ExtractOutputPreprocessor
-from traitlets.config import Config
-import jupytext
-import os
-
-log = getLogger("mkdocs.plugins.execute")
-log.setLevel("INFO")
-
-output_extractor = ExtractOutputPreprocessor()
-output_extractor.extract_output_types = (
-    output_extractor.extract_output_types
-    | {'application/vnd.plotly.v1+json'}
-)
-
-
-class AlreadySavedFile(File):
-    def copy_file(self, dirty=False):
-        pass
-
-
-exporter = nbconvert.TemplateExporter(
-    config=Config(dict(
-        TemplateExporter=dict(
-            preprocessors=[
-                nbconvert.preprocessors.ExecutePreprocessor,
-                output_extractor,
-            ],
-            exclude_input=False,
-            extra_template_basedirs=[str(Path(__file__).parent / "templates")],
-            template_file='mkdocs_markdown/index.md.j2',
-        ),
-        NbConvertBase=dict(
-            display_data_priority=[
-                'application/vnd.plotly.v1+json',
-                'text/html',
-                'text/markdown',
-                'image/svg+xml',
-                'text/latex',
-                'image/png',
-                'image/jpeg',
-                'text/plain'
-            ]
-        ),
-    ))
-)
-writer = nbconvert.writers.FilesWriter(build_directory=str())
-
-
-class Plugin(BasePlugin):
-    def __init__(self):
-        self.output_map = {}
-
-    def on_page_read_source(
-        self, page, config, **kwargs
-    ):
-        os.environ["PLOTLY_RENDERER"] = "plotly_mimetype"
-        src_path = page.file.abs_src_path
-        notebook = jupytext.read(src_path)
-        log.info(f"Executing {src_path}")
-        output, resources = exporter.from_notebook_node(
-            notebook,
-            resources={
-                "unique_key": page.file.src_path,
-                # Compute the relative URL
-                "output_files_dir": "_execute_outputs",
-                "metadata": {
-                    "path": Path(src_path).parent
-                }
-            }
-        )
-        build_directory = Path(config["site_dir"])
-        nbconvert.writers.FilesWriter(
-            build_directory=str(build_directory)
-        ).write(output, resources, "out.md")
-        out = build_directory / "out.md"
-        source = out.read_text()
-        out.unlink()
-        self.output_map[src_path] = list(resources["outputs"].keys())
-        return source
-
-    def on_page_markdown(self, markdown, page, config, files):
-        src_path = page.file.abs_src_path
-        for file in self.output_map.pop(page.file.abs_src_path):
-            files.append(
-                AlreadySavedFile(
-                    str(file),
-                    config['docs_dir'],
-                    config['site_dir'],
-                    config['use_directory_urls']
-                )
-            )
-
-
-plugin_instance = Plugin()
-on_page_read_source = plugin_instance.on_page_read_source
-on_page_markdown = plugin_instance.on_page_markdown
\ No newline at end of file

mkdocs.yml

@@ -62,6 +62,10 @@ theme:
 plugins:
   - search
   - social
+  - execute:
+      include: ["*.md"]
+      execute_without_tag: ["*.md"]
+      markdown_template: 'templates/mkdocs_markdown/index.md.j2'
 
 markdown_extensions:
   - pymdownx.arithmatex:
@@ -77,15 +81,12 @@ markdown_extensions:
   - footnotes
   - meta
 
-hooks:
-  - execute.py
-
 extra_javascript:
   - scripts/katex.js
   - scripts/plotlyhelper.js
   - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/katex.min.js
   - https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.16.7/contrib/auto-render.min.js
-  - 'https://polyfill.io/v3/polyfill.min.js?features=es6'
+  - 'https://cdnjs.cloudflare.com/polyfill/v3/polyfill.min.js?features=es6'
   - 'https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js'
   - 'https://cdn.plot.ly/plotly-latest.min.js'
 

pixi.toml

+[project]
+authors = ["Open solid state notes authors"]
+channels = ["conda-forge"]
+description = "Lecture notes on solid state physics"
+name = "Open solid state notes"
+platforms = ["linux-64", "osx-64", "win-64"]
+version = "0.1.0"
+
+[tasks]
+build = { cmd="mkdocs build", env ={PYDEVD_DISABLE_FILE_VALIDATION="1", JUPYTER_PLATFORM_DIRS="1"}}
+
+[dependencies]
+ipykernel = ">=6.29.5,<7"
+plotly = ">=5.23.0,<6"
+scipy = ">=1.14.1,<2"
+numpy = ">=2.1.0,<3"
+matplotlib = ">=3.9.2,<4"
+mkdocs = ">=1.6.0,<2"
+mkdocs-material = ">=9.5.33,<10"
+python-markdown-math = ">=0.8,<0.9"
+pillow = ">=10.4.0,<11"
+cairosvg = ">=2.7.1,<3"
+pandas = ">=2.2.2,<3"
+ffmpeg = ">=7.0.2,<8"
+
+[pypi-dependencies]
+wikitables = ">=0.5.5, <0.6"
+mkdocs-execute-plugin = ">=0.0.8, <0.1.0"