Some progress in Phys excph

.gitignore

@@ -3,4 +3,4 @@ build
 *.egg-info
 dist
 .DS_store
-git.sh
+docs/QuREX-book/_build/

AUTHORS.md

@@ -6,7 +6,7 @@ Project Authors
 * Paleari, Fulvio, Istituto Nanoscienze (Italy)
 * Molina-Sánchez, Alejandro, Universitat de València (Spain)
 * Nalabothula, Muralidhar, University of Luxembourg (Luxembourg)
-* Reho, Riccardo, Utrecht University (Netherlands)
+* Reho, Riccardo, University of Luxembourg (Luxembourg)
 * Bonacci, Miki, Paul Scherrer Institute (Switzerland)
 * Castelo, José, Universitat de València (Spain)
 * Cervantes-Villanueva, Jorge, Universitat de València (Spain)
@@ -23,4 +23,5 @@ Project Authors
 * Davide Romanin
 * Daniel Murphy
 * Yuncheng Mao
-
+* Marco D'Alessandro
+* Daniel Santos Stone

docs/Makebook

@@ -0,0 +1,2 @@
+#sphinx-build source/ build/
+jupyter-book build QuREX-book/

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/QuREX-book/_config.yml

@@ -0,0 +1,32 @@
+title: "QuREX Documentation"
+author: "Riccardo Reho"
+
+sphinx:
+  config:
+    bibtex_reference_style: author_year
+
+    # Enable equation numbering and styling like LaTeX
+    mathjax_config:
+      tex:
+        tags: "none"            # Number all displayed equations
+        tagSide: "right"       # Equation numbers on the right
+        tagIndent: "0.8em"     # Spacing before equation numbers
+
+    # Enable MyST extensions for advanced math and referencing
+    myst_enable_extensions:
+      - amsmath               # Enables environments like align, gather
+      - dollarmath            # Inline and block LaTeX with $...$ or $$...$$
+      - deflist               # (Optional) Definition lists
+      - linkify               # Auto-detect links
+      - substitutions         # Enable |substitution| syntax
+      - colon_fence           # For ::: fenced blocks (like admonitions)
+      - smartquotes           # Typographic quotes
+
+  extra_extensions:
+    - sphinxcontrib.bibtex    # For citations and references
+
+bibtex_bibfiles:
+  - references.bib            # Your BibTeX file
+
+parse:
+  myst_extended_syntax: true

docs/QuREX-book/_toc.yml

@@ -0,0 +1,40 @@
+format: jb-book
+root: intro  # The landing page (intro.md)
+options:
+  numbered: true  # Enable numbering globally
+
+parts:
+- caption: Theory
+  numbered: false  # Ensure numbering applies to this part
+  chapters:
+    - file: content/theory/theoretical_background  # Acts as the section's intro
+      sections:
+        - file: content/theory/model_hamiltonian
+        - file: content/theory/coulomb_potential
+        - file: content/theory/h2p
+        - file: content/theory/wannier_exciton
+        - file: content/theory/wannier_chern
+        - file: content/theory/wannier_basis
+        - file: content/theory/quantum_well
+        - file: content/theory/exciton_phonon_coupling
+- caption: Software
+  numbered: false
+  chapters:
+    - file: content/software/software
+      sections:
+        - file: content/software/yambo/yambo
+        - file: content/software/yambo/yambo_input_flags 
+- caption: Tutorials
+  numbered: false
+  chapters:
+    - file: content/tutorials/tutorials
+      sections:
+        - file: content/tutorials/exciton_phonon
+
+- caption: Notebooks
+  numbered: false
+  execute: 
+    execute_notebooks: 'off'
+  chapters:
+    - file: notebooks/notebooks
+    - file: notebooks/exciton_phonon

docs/QuREX-book/bse_equation.md

@@ -0,0 +1,37 @@
+# BSE Equation
+
+The Bethe-Salper Equations (BSE) allows computing neutral excitations for electron-hole interactions.
+Following the Ai-MBPT formalism {cite}`sangalli2019many, marini2009yambo` the exciton energies and wavefunctions, are obtained solving the BSE equation in the Tamm-Dancoff approximation including local field effects {cite}`onida2002electronic`. 
+
+The BSE can be recast into an eigenvalue equation 
+
+$$
+    \left(\varepsilon_{c\mathbf{k}}^{\mathrm{GW}}
+    -\varepsilon_{\mathrm{v}\mathbf{k-Q}}^{\mathrm{GW}}\right)
+    A_{\mathrm{vc}\mathbf{k}}^\lambda+\sum_{\mathbf{k}^{\prime}
+    c^{\prime} \mathbf{v}^{\prime}}
+    K_{\substack{\mathrm{vc\mathbf{k}} \\ v^{\prime} c^{\prime} \mathbf{k}^{\prime}}}^{\mathbf{Q}}
+    A_{v^{\prime} c^{\prime} \mathbf{k}^{\prime}}^{\lambda,\mathbf{Q}}
+    =E_{\lambda,\mathbf{Q}} A_{v c \mathbf{k}}^{\lambda,\mathbf{Q}}
+$$ (eq-BSE)
+
+where $\varepsilon_{c\mathbf{k}/v\mathbf{k}}$ are quasi-particle band energies, 
+ $A^{\lambda}_{v c\mathbf{k}}$ are the BSE coefficients, $E_{\lambda,\mathbf{Q}}$ %are 
+the energy of exciton $\lambda$, and $\mathbf{Q}$ the momentum transfer between an electron at $\mathbf{k}$ and a hole at $\mathbf{k-Q}$.
+The kernel $K$ contains the electron-hole Coulomb interaction matrix elements, which is the sum of the direct $K^{d}$ and exchange $K^{x}$ terms and can be written as
+$$
+    K_{\substack{\mathrm{vc\mathbf{k}} \\ v^{\prime} c^{\prime} \mathbf{k}^{\prime}}}^{\mathbf{Q}} =     K_{\substack{\mathrm{vc\mathbf{k}} \\ v^{\prime} c^{\prime} \mathbf{k}^{\prime}}}^{d,\mathbf{Q}} +     K_{\substack{\mathrm{vc\mathbf{k}} \\ v^{\prime} c^{\prime} \mathbf{k}^{\prime}}}^{x,\mathbf{Q}}
+$$
+
+Following the prescription of \textit{Dias et al.} {cite}`dias2023wantibexos`} we can compute the direct and exchange terms as follows:
+
+$$
+    K_{\substack{\mathrm{vc\mathbf{k}} \\ v^{\prime} c^{\prime} \mathbf{k}^{\prime}}}^{d,\mathbf{Q}} = V(\mathbf{k}-\mathbf{k}^\prime)\langle
+    c,\mathbf{k}|
+    c^\prime,\mathbf{k}^\prime\rangle\langle
+    v^\prime, \mathbf{k}^\prime-\mathbf{Q}|v\mathbf{k-Q}\rangle \\
+    K_{\substack{\mathrm{vc\mathbf{k}} \\ v^{\prime} c^{\prime} \mathbf{k}^{\prime}}}^{x,\mathbf{Q}} = -V(\mathbf{k}-\mathbf{k}^\prime)\langle
+    c,\mathbf{k}|
+    v,\mathbf{k}-\mathbf{Q}\rangle\langle
+    v^\prime, \mathbf{k}^\prime-\mathbf{Q}|c^\prime\mathbf{k}^\prime-\mathbf{Q}\rangle \\    
+$$ (eq:kernels)

docs/QuREX-book/conf.py

@@ -0,0 +1,51 @@
+###############################################################################
+# Auto-generated by `jupyter-book config`
+# If you wish to continue using _config.yml, make edits to that file and
+# re-generate this one.
+###############################################################################
+author = 'Henrique Miranda, Alejandro Molina Sánchez, Fulvio Paleari, Riccardo Reho'
+comments_config = {'hypothesis': False, 'utterances': False}
+copyright = '2024, Henrique Miranda, Alejandro Molina Sánchez, Fulvio Paleari, Riccardo Reho'
+exclude_patterns = ['build', 'Thumbs.db', '.DS_Store']
+extensions = [
+    'sphinx.ext.autodoc',
+    'sphinx.ext.autosummary',
+    'sphinx.ext.todo',
+    'sphinx.ext.coverage',
+    'sphinx.ext.mathjax',
+    'sphinx.ext.ifconfig',
+    'sphinx.ext.viewcode',
+    'sphinx_jupyterbook_latex',
+    'sphinx_multitoc_numbering',
+    'sphinxcontrib.bibtex',
+    'sphinx_proof'
+]
+external_toc_exclude_missing = False
+external_toc_path = '_toc.yml'
+html_baseurl = ''
+html_favicon = '../logos/yambopy_square.png'
+html_logo = ''
+html_sidebars = {'**': ['globaltoc.html', 'relations.html', 'sourcelink.html', 'searchbox.html']}
+html_sourcelink_suffix = ''
+html_theme = 'sphinx_book_theme'
+html_theme_options = {'search_bar_text': 'Search this book...', 'launch_buttons': {'notebook_interface': 'classic', 'binderhub_url': '', 'jupyterhub_url': '', 'thebe': False, 'colab_url': '', 'deepnote_url': ''}, 'path_to_docs': '', 'repository_url': 'https://github.com/executablebooks/jupyter-book', 'repository_branch': 'master', 'extra_footer': '', 'home_page_in_toc': True, 'announcement': '', 'analytics': {'google_analytics_id': '', 'plausible_analytics_domain': '', 'plausible_analytics_url': 'https://plausible.io/js/script.js'}, 'use_repository_button': False, 'use_edit_page_button': False, 'use_issues_button': False}
+html_title = 'QuREX Documentation'
+latex_engine = 'pdflatex'
+myst_enable_extensions = ['colon_fence', 'dollarmath', 'linkify', 'substitution', 'tasklist']
+myst_url_schemes = ['mailto', 'http', 'https']
+nb_execution_allow_errors = False
+nb_execution_cache_path = ''
+nb_execution_excludepatterns = []
+nb_execution_in_temp = False
+nb_execution_mode = 'auto'
+nb_execution_timeout = 30
+nb_output_stderr = 'show'
+numfig = True
+project = 'yambopy'
+pygments_style = 'sphinx'
+release = '3.0.0'
+suppress_warnings = ['myst.domains']
+sys_path = ['../../yambopy']
+templates_path = ['_templates']
+use_jupyterbook_latex = True
+use_multitoc_numbering = True

docs/QuREX-book/content/software/software.md

@@ -0,0 +1 @@
+# Software

docs/QuREX-book/content/software/yambo/yambo.md

@@ -0,0 +1 @@
+# Yambo