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📚 Docs: switch to sphinx book theme
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@bastonero
bastonero committed Feb 16, 2025
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31 changes: 19 additions & 12 deletions docs/source/conf.py
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@@ -1,16 +1,11 @@
# -*- coding: utf-8 -*-
#
# aiida-wannier90 documentation build configuration file, created by
# sphinx-quickstart on Fri Oct 10 02:14:52 2014.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All configuration values have a default; values that are commented out
# serve to show the default.
#
"""Configuration file for the documentation."""
import pathlib
import time
Expand All @@ -29,10 +24,10 @@

project = 'aiida-hubbard'
copyright = ( # pylint: disable=redefined-builtin, line-too-long
f"""2022-{time.localtime().tm_year}, UNIVERSITY OF BREMEN, Germany,"""
"""and ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of"""
"""Materials (THEOS) and National Centre for Computational Design and Discovery"""
"""of Novel Materials (NCCR MARVEL)), Switzerland. All rights reserved"""
f"""2022-{time.localtime().tm_year}, University of Bremen, Germany, U Bremen Excellence Chair;
Authors: Lorenzo Bastonero. Paul Scherrer Institut, Switzerland, Laboratory of Materials Simulations;
Authors: Giovanni Pizzi. ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE, Switzerland, Laboratory of Theory
and Simulation of Materials (THEOS); Authors: Sebastiaan Huber, Nicola Marzari."""
) # pylint: disable=redefined-builtin, line-too-long

# The full version, including alpha/beta/rc tags.
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'aiida_pseudo': ('http://aiida-pseudo.readthedocs.io/en/latest/', None),
'aiida_quantumespresso': ('http://aiida-quantumespresso.readthedocs.io/en/latest/', None),
'sphinx': ('https://www.sphinx-doc.org/en/master', None),
'matplotlib': ('https://matplotlib.org/stable/', None),
}

myst_enable_extensions = [
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# The theme to use for HTML and HTML Help pages. See the documentation for
# a list of builtin themes.

html_theme = 'pydata_sphinx_theme'
html_theme = 'sphinx_book_theme'
html_theme_options = {
'github_url': 'https://github.com/aiidateam/aiida-hubbard',
'twitter_url': 'https://twitter.com/aiidateam',
'use_edit_page_button': True,
'use_download_button': True,
'use_sidenotes': True,
'logo': {
'text': 'AiiDA Hubbard',
'image_light': 'images/logo_aiida_quantumespresso.png',
'image_dark': 'images/logo_aiida_quantumespresso.png',
}
}
html_static_path = ['_static']
html_context = {
'github_user': 'aiidateam',
'github_user': 'bastonero',
'github_repo': 'aiida-hubbard',
'github_version': 'main',
'doc_path': 'docs/source',
'default_mode': 'light',
}
html_sidebars = {
'**': ['navbar-logo.html', 'navbar-icon-links.html', 'search-field.html', 'sbt-sidebar-nav.html']
}

# The name of an image file (relative to this directory) to place at the top
# of the sidebar.
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r'phonopy.*',
r'numpy.*',
r'np.*',
r'pydantic.*',
]
]
115 changes: 30 additions & 85 deletions docs/source/index.md
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Expand Up @@ -11,43 +11,37 @@ myst:

```{toctree}
:hidden: true
:maxdepth: 2
installation/index
tutorials/index
howto/index
topics/index
reference/index
```

::::{grid}
:reverse:
:gutter: 2 3 3 3
:margin: 1 2 1 2

:::{grid-item}
:columns: 12 4 4 4
```{toctree}
:hidden: true
:caption: How to Guides
```{image} images/logo_aiida_quantumespresso.png
:width: 200px
:class: sd-m-auto
howto/index
citeus
```
:::

:::{grid-item}
:columns: 12 8 8 8
:child-align: justify
:class: sd-fs-5
```{toctree}
:hidden: true
:caption: Topic guides
topics/index
```

# AiiDA Quantum ESPRESSO HP
```{toctree}
:hidden: true
:caption: Reference
reference/index
```

An AiiDA plugin package for the calculation of Hubbard parameters using the [Quantum ESPRESSO](http://www.quantumespresso.org) software suite. Compute onsites and intersites Hubbard parameters self-consistently and in automated fashion through state-of-the-art DFPT implementation with automatic data provenance provided by AiiDA.

**aiida-hubbard version:** {{ release }}
# AiiDA Hubbard

:::
An AiiDA plugin package for the calculation of Hubbard parameters from first-principles using the [Quantum ESPRESSO](http://www.quantumespresso.org) and HP software suite. Compute onsites and intersites Hubbard parameters self-consistently and in automated fashion through state-of-the-art DFPT implementation, leveraging maximal parallel computation over atoms and monochromatic perturbations, along with data provenance provided by AiiDA.

::::
**aiida-hubbard version:** {{ release }}

______________________________________________________________________

Expand Down Expand Up @@ -92,78 +86,29 @@ Easy examples to take the first steps with the plugin package.
To the tutorials
```
:::
::::

:::{grid-item-card} {fa}`question-circle;mr-1` How-to guides
:text-align: center
:shadow: md

Hands-on guides to achieve specific goals.

+++

```{button-ref} howto/index
:ref-type: doc
:click-parent:
:expand:
:color: primary
:outline:
To the how-to guides
```
:::

:::{grid-item-card} {fa}`bookmark;mr-1` Topic guides
:text-align: center
:shadow: md

Detailed background information on various concepts.

+++

```{button-ref} topics/index
:ref-type: doc
:click-parent:
:expand:
:color: primary
:outline:
To the topic guides
```
:::

:::{grid-item-card} {fa}`cogs;mr-1` Reference guides
:text-align: center
:shadow: md

Detailed reference guides on the application programming and command line interfaces.
# How to cite

+++
If you use this plugin for your research, please cite the following works:

```{button-ref} reference/api/aiida_hubbard/index
:ref-type: doc
:click-parent:
:expand:
:color: primary
:outline:
> Lorenzo Bastonero, Cristiano Malica, Eric Macke, Marnik Bercx, Sebastiaan Huber, Iurii Timrov, and Nicola Marzari, *Hubbard from first-principles made easy from automated and reproducible workflows* (2025)
To the reference guides
```
:::
::::
> Sebastiaan. P. Huber _et al._, [*AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance*](https://doi.org/10.1038/s41597-020-00638-4), Scientific Data **7**, 300 (2020)
# How to cite
> Martin Uhrin, Sebastiaan. P. Huber, Jusong Yu, Nicola Marzari, and Giovanni Pizzi, [*Workflows in AiiDA: Engineering a high-throughput, event-based engine for robust and modular computational workflows*](https://www.sciencedirect.com/science/article/pii/S0010465522001746), Computational Materials Science **187**, 110086 (2021)
If you use this plugin for your research, please cite the following work:
Please, also cite the relevant _Quantum ESPRESSO_ and _HP_ references.

> Lorenzo Bastonero, Cristiano Malica, Marnik Bercx, Eric Macke, Iurii Timrov, Nicola Marzari, and Sebastiaan P. Huber, [*Automated self-consistent prediction of extended Hubbard parameters for Li-ion batteries*](https://media.giphy.com/media/zyclIRxMwlY40/giphy.gif), npj Comp. Mat., **?**, ? (2023)
> Iurii Timrov, Nicola Marzari, and Matteo Cococcioni, [*HP – A code for the calculation of Hubbard parameters using density-functional perturbation theory*](https://www.sciencedirect.com/science/article/pii/S0010465522001746), Computer Physics Communication **279**, 108455 (2022)
> Sebastiaan. P. Huber, Spyros Zoupanos, Martin Uhrin, Leopold Talirz, Leonid Kahle, Rico Häuselmann, Dominik Gresch, Tiziano Müller, Aliaksandr V. Yakutovich, Casper W. Andersen, Francisco F. Ramirez, Carl S. Adorf, Fernando Gargiulo, Snehal Kumbhar, Elsa Passaro, Conrad Johnston, Andrius Merkys, Andrea Cepellotti, Nicolas Mounet, Nicola Marzari, Boris Kozinsky, and Giovanni Pizzi, [*AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance*](https://doi.org/10.1038/s41597-020-00638-4), Scientific Data **7**, 300 (2020)
> Paolo Giannozzi _et al._, [*Advanced capabilities for materials modelling with Quantum ESPRESSO*](https://iopscience.iop.org/article/10.1088/1361-648X/aa8f79) J.Phys.:Condens.Matter **29**, 465901 (2017)
> Martin Uhrin, Sebastiaan. P. Huber, Jusong Yu, Nicola Marzari, and Giovanni Pizzi, [*Workflows in AiiDA: Engineering a high-throughput, event-based engine for robust and modular computational workflows*](https://www.sciencedirect.com/science/article/pii/S0010465522001746), Computational Materials Science **187**, 110086 (2021)
> Paolo Giannozzi _et al._, [*QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials*](https://iopscience.iop.org/article/10.1088/0953-8984/21/39/395502) J. Phys. Condens. Matter **21**, 395502 (2009)
> Iurii Timrov, Nicola Marzari, and Matteo Cococcioni, [*HP - A code for the calculation of Hubbard parameters using density-functional perturbation theory*](https://doi.org/10.1016/j.commatsci.2020.110086), Computational Materials Science **187**, 110086 (2021)
For the GPU-enabled version of _Quantum ESPRESSO_:

> Iurii Timrov, Nicola Marzari, and Matteo Cococcioni, [*Self-consistent Hubbard parameters from density-functional perturbation theory in the ultrasoft and projector-augmented wave formulations*](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.103.045141), Physical Reveview **B** **103**, 045141
> Paolo Giannozzi _et al._, [*Quantum ESPRESSO toward the exascale*](https://pubs.aip.org/aip/jcp/article/152/15/154105/1058748/Quantum-ESPRESSO-toward-the-exascale), J. Chem. Phys. **152**, 154105 (2020)
# Acknowledgements

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