diff --git a/source/_static/AuNP.png b/source/_static/AuNP.png index 65bb45df..763e8caa 100644 Binary files a/source/_static/AuNP.png and b/source/_static/AuNP.png differ diff --git a/source/_static/C180.png b/source/_static/C180.png index df9dfbfc..586da676 100644 Binary files a/source/_static/C180.png and b/source/_static/C180.png differ diff --git a/source/_static/benzene-mo.png b/source/_static/benzene-mo.png index 1db77fe2..c58d6024 100644 Binary files a/source/_static/benzene-mo.png and b/source/_static/benzene-mo.png differ diff --git a/source/_static/bondcentric.png b/source/_static/bondcentric.png index 1602ea87..aa0cad86 100644 Binary files a/source/_static/bondcentric.png and b/source/_static/bondcentric.png differ diff --git a/source/_static/covid-spike.png b/source/_static/covid-spike.png index 2566af0d..2043e315 100644 Binary files a/source/_static/covid-spike.png and b/source/_static/covid-spike.png differ diff --git a/source/_static/ferrocene.png b/source/_static/ferrocene.png index 9a78dae2..6fd5b738 100644 Binary files a/source/_static/ferrocene.png and b/source/_static/ferrocene.png differ diff --git a/source/_static/home_screenshot_1.png b/source/_static/home_screenshot_1.png new file mode 100644 index 00000000..03165564 Binary files /dev/null and b/source/_static/home_screenshot_1.png differ diff --git a/source/_static/home_splash_1.png b/source/_static/home_splash_1.png new file mode 100644 index 00000000..426b6b11 Binary files /dev/null and b/source/_static/home_splash_1.png differ diff --git a/source/_static/phenol-qtaim.png b/source/_static/phenol-qtaim.png index 720329f2..f835d18b 100644 Binary files a/source/_static/phenol-qtaim.png and b/source/_static/phenol-qtaim.png differ diff --git a/source/_static/zeolite.png b/source/_static/zeolite.png index 720e6b9a..0b887a08 100644 Binary files a/source/_static/zeolite.png and b/source/_static/zeolite.png differ diff --git a/source/docs/index.md b/source/docs/index.md index 8ba3addd..55e526da 100644 --- a/source/docs/index.md +++ b/source/docs/index.md @@ -2,23 +2,43 @@ # Guide -Avogadro is a free, open-source molecular editor and visualization tool, designed for use on Mac, Windows, and Linux in computational chemistry, molecular modeling, chemistry education, bioinformatics, materials science, and related areas. It offers flexible high-quality rendering and a powerful plugin architecture. +Avogadro is an advanced free and open source molecular editor and visualization tool. + +It is highly capable and designed for use in computational chemistry, molecular modeling, chemistry education, bioinformatics, materials science, and related areas. + +It offers flexible high-quality rendering, a modern UI with native styling, and a powerful plugin architecture. + +Avogadro is designed for cross-platform use and is fully supported on Windows, Linux, and macOS. ## Avogadro 2 -In particular, this manual covers the new release of Avogadro 2, a major update, and includes major changes, the revised interface, and new features. Most sections include notes on changes from v1.0, 1.1, and 1.2 to the new 2.0 release. +In particular, this manual covers the new release of Avogadro 2, a major update, and includes major changes, the revised interface, and new features. +Most sections include notes on changes from v1.0, 1.1, and 1.2 to the new 2.0 release, though as there have been so many, coverage is not in any way comprehensive. -For new features, a "**New in 2.0**" heading is included. +Versions 1.90 to 1.99 were beta releases of Avogadro 2 and a lot of this manual applied to those versions too, but note that during the beta phase there were also many improvements made to the UI which have changed the location or appearance of various things. -The revised manual also includes tips and warnings as call-out sections: +Look out for boxes highlighting new features or changes for Avogadro 2: -```{warning} -This is a warning – pay attention to something that may cause problems -``` +:::{versionadded} 2.0 +::: -```{tip} -This is a tip – something that can help you work better -``` +:::{versionchanged} 2.0 +This feature now behaves differently. +::: + +The revised manual also includes annotations: + +:::{warning} +This is a warning -- something that may cause problems. +::: + +:::{tip} +This is a tip -- something that can help you work better. +::: + +:::{note} +This is a note -- further relevant information. +::: ## Thanks @@ -27,7 +47,7 @@ This book would not be possible without the help and effort of many people, incl Initial funding for the Avogadro manual was provided by the [University of Pittsburgh Department of Chemistry](http://www.chem.pitt.edu/). * Version 1 - Summer 2015 - Taylor Cornell and Geoffrey Hutchison -* Version 2 - 2022-204 - Geoffrey Hutchison +* Version 2 - 2022-2024 - Geoffrey Hutchison and Matt Milner ```{toctree} --- diff --git a/source/index.md b/source/index.md index 54f8ee41..b1cd5769 100644 --- a/source/index.md +++ b/source/index.md @@ -5,133 +5,396 @@ html_theme.show_prev_next: false --- (about)= +# Avogadro -Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture. +% One top-level grid with only rows, so that each text card is always next to the correct picture +:::::::{grid} 1 +:gutter: 5 +:padding: 5 -This documentation site is for Avogadro 2, currently in development. +% Now each row should be an adaptive grid, so that the text and image are side by side on monitors but stacked on mobile +% Use reverse for rows where the picture should be on the left +::::::{grid} 1 1 2 2 +:gutter: 5 -::::{card-carousel} 3 -:::{card} -![Thumbnail for benzene molecular orbital](/_static/benzene-mo.png) -::: -:::{card} -![Thumbnail for zeolite rendering](/_static/zeolite.png) -::: -:::{card} -![Thumbnail for COVID spike protein](/_static/covid-spike.png) -::: -:::{card} -![Thumbnail for COVID spike protein](/_static/AuNP.png) +:::::{grid} 1 +:gutter: 5 + +% Yet another nested grid so that the headline text and button are stacked +::::{grid-item} +:class: sd-font-weight-bold sd-fs-3 sd-text-primary +A free and open source molecular editor and visualization tool. +:::: + +::::{grid-item} +:::{button-ref} install +:color: primary +:shadow: +:expand: +Get Avogadro ::: -:::{card} -![Thumbnail for bond-centric editing](/_static/bondcentric.png) +:::: +::::: + +:::::{grid-item-card} +:class-card: sd-border-0 +:shadow: none +:img-background: /_static/home_screenshot_1.png +::::: +:::::: + +% Next row +::::::{grid} 1 1 2 2 +:gutter: 5 +:reverse: + +:::::{grid-item-card} Flexible +:class-card: sd-border-0 +:shadow: none +:class-title: sd-fs-4 sd-text-primary +Designed for students and advanced researchers alike. + +Used in computational chemistry, molecular modeling, chemistry education, bioinformatics, materials science, and more. + +Molecules, crystals, biomolecules, surfaces -- Avogadro loves them all. +::::: + +:::::{grid-item-card} +:class-card: sd-border-0 +:img-background: /_static/home_splash_1.png +:img-alt: Benzene with rendered molecular orbital +::::: +:::::: + +% Next row +::::::{grid} 1 1 2 2 +:gutter: 5 + +:::::{grid-item-card} Intuitive +:class-card: sd-border-0 +:shadow: none +:class-title: sd-fs-4 sd-text-primary +A sleek interface and user-friendly tools makes working in Avogadro easy, whether you are playing with molecules in 3D for the first time, quickly sketching structures for calculation input, or preparing graphics for publication. +::::: + +:::::{grid-item-card} +:img-background: /_static/bondcentric.png +:img-alt: Bond-centric manipulation of a molecule +::::: +:::::: + +% Next row +::::::{grid} 1 1 2 2 +:gutter: 5 +:reverse: + +:::::{grid-item-card} Beautiful +:class-card: sd-border-0 +:shadow: none +:class-title: sd-fs-4 sd-text-primary +With a new, modern 3D renderer, visual effects like reflections and ambient occlusion, and a variety of display options, your molecules look good in Avogadro. + +A picture paints a thousand words, but a movie tells a story -- make an animation to bring your chemistry to life. +::::: + +:::::{grid-item-card} +:img-background: /_static/ferrocene.png +:img-alt: Ferrocene +::::: +:::::: + +% Next row +::::::{grid} 1 1 2 2 +:gutter: 5 + +:::::{grid-item-card} Fast +:class-card: sd-border-0 +:shadow: none +:class-title: sd-fs-4 sd-text-primary +Thanks to the rewritten core and lightning-quick multithreaded renderer, Avogadro 2 handles systems of thousands of atoms effortlessly. + +Built-in force fields tidy up hand-drawn molecules in seconds. +::::: + +:::::{grid-item-card} +:img-background: /_static/covid-spike.png +:img-alt: COVID-19 spike protein +::::: +:::::: + +% Next row +::::::{grid} 1 1 2 2 +:gutter: 5 +:reverse: + +:::::{grid-item-card} Compatible +:class-card: sd-border-0 +:shadow: none +:class-title: sd-fs-4 sd-text-primary +Read your geometry files, wherever they are from -- Avogadro understands a huge number of file formats, and can write to hundreds. + +Explore the results of calculations with native output parsing for popular quantum chemistry programs including GAMESS, Gaussian, Molden, MOPAC, NWChem, and ORCA. +::::: +% Replace with a fancier looking molecular orbital render of some kind +:::::{grid-item-card} +:img-background: /_static/benzene-mo.png +:img-alt: Benzene with rendered molecular orbital +::::: +:::::: + +% Next row +::::::{grid} 1 1 2 2 +:gutter: 5 + +:::::{grid-item-card} Extensible +:class-card: sd-border-0 +:shadow: none +:class-title: sd-fs-4 sd-text-primary +Plugins add diverse functionality -- interactive tools, commands, interfaces to other programs, additional force fields and file formats, and more. + +Writing your own plugin in Python is straightforward. +And if it's useful, why not share it with the community? +::::: + +:::::{grid-item-card} +:img-background: /_static/zeolite.png +:img-alt: Zeolite rendering +::::: +:::::: + +% Next row +::::::{grid} 1 1 2 2 +:gutter: 5 +:reverse: + +:::::{grid-item-card} Open +:class-card: sd-border-0 +:shadow: none +:class-title: sd-fs-4 sd-text-primary +Avogadro is _free_, and all source code and documentation is available under the permissive BSD 3-clause license. + +Got an issue? +The Avogadro community is friendly and ready to help. + +Got an idea? +Development is public and contributions are welcomed. +::::: + +:::::{grid-item-card} +:img-background: /_static/AuNP.png +:img-alt: A gold nanoparticle +::::: +:::::: + +% Next row +::::::{grid} 1 1 2 2 +:gutter: 5 + +:::::{grid-item-card} International +:class-card: sd-border-0 +:shadow: none +:class-title: sd-fs-4 sd-text-primary +Translations available for Simplified Chinese, English, Esperanto, French, Georgian, German, Hungarian, Japanese, Korean, Portuguese, Romanian, Serbian, and Turkish, with [more languages being added all the time](https://hosted.weblate.org/engage/avogadro/). +::::: + +:::::{grid-item-card} +:img-background: /_static/C180.png +:img-alt: Symmetry analysis of C180 +::::: +:::::: + +% Next row +::::::{grid} 1 1 2 2 +:gutter: 5 +:reverse: + +:::::{grid-item-card} Cross-platform +:class-card: sd-border-0 +:shadow: none +:class-title: sd-fs-4 sd-text-primary +Whether you use Windows, Linux, or macOS to get your work done, Avogadro is available and supported. + +On ARM? +Apple Silicon is already supported, with Windows on ARM a future target. + +The Qt base means Avogadro looks native and fits right in on your desktop. +::::: + +:::::{grid-item-card} +:img-background: /_static/phenol-qtaim.png +:img-alt: QTAim analysis +::::: +:::::: + +::::::: + + +:::{button-ref} install +:color: primary +:shadow: +:expand: +Get Avogadro ::: -:::{card} -![Thumbnail for symmetry analysis of C180](/_static/C180.png) + + +## Resources + +:::::{grid} 1 2 3 3 +:gutter: 3 +:class-row: sd-align-major-center + +::::{grid-item-card} +:class-header: sd-font-weight-bold sd-bg-light sd-text-center sd-text-dark +:class-body: sd-text-center +{fas}`book;fa-2x` User Guide +^^^ + +Read the documentation and learn how to use Avogadro: + +:::{button-ref} docs +:color: primary +:shadow: +:align: center +Guide ::: -:::{card} -![Thumbnail for ferrocene](/_static/ferrocene.png) +:::{button-ref} getting-started +:color: primary +:outline: +:align: center +Getting started ::: -:::{card} -![Thumbnail for QTAim analysis](/_static/phenol-qtaim.png) +:::{button-ref} tutorials +:color: primary +:outline: +:align: center +Tutorials ::: :::: -## Install -::::{grid} 3 -:::{grid-item-card} -:text-align: center -:class-header: sd-font-weight-bold sd-bg-light -{fab}`apple;fa-2x` MacOS +::::{grid-item-card} +:class-header: sd-font-weight-bold sd-bg-light sd-text-center sd-text-dark +:class-body: sd-text-center +{fas}`laptop-code;fa-2x` Development ^^^ -{{ 'Download DMG'}} -++++ -Download Nightly Build -::: -:::{grid-item-card} -:text-align: center -:class-header: sd-font-weight-bold sd-bg-light -{fab}`windows;fa-2x` Windows -^^^ -{{ 'Download Installer'}} -++++ -Download Nightly Build -::: +Write Python scripts and C++ code for Avogadro: -:::{grid-item-card} -:text-align: center -:class-header: sd-font-weight-bold sd-bg-light -{fab}`linux;fa-2x` Linux -^^^ -{{ 'Download AppImage'}} -++++ -Build from source +:::{button-ref} develop +:color: primary +:shadow: +:align: center +Develop +::: +:::{button-ref} develop-scripts +:color: primary +:outline: +:align: center +Scripts +::: +:::{button-ref} develop-classlist +:color: primary +:outline: +:align: center +C++ API ::: - :::: -## Features - -- Free, Open Source: Easy to install and all source code and documentation is available to modify or extend. -- International: Translations into English, French, German, Hungarian, Indonesian, Japanese, Portuguese, Serbian, Turkish, and others, with [more languages to come](https://hosted.weblate.org/engage/avogadro/). -- Intuitive: Built to work easily for students and advanced researchers both. -- Fast: Supports multi-threaded rendering and computation. -- Extensible: Plugin architecture for developers, including rendering, interactive tools, commands, and Python scripts. - -## Resources -::::{grid} 3 -:::{grid-item-card} -:class-header: sd-font-weight-bold sd-bg-light sd-text-center -{fas}`book;fa-2x` User Guide +::::{grid-item-card} +:class-header: sd-font-weight-bold sd-bg-light sd-text-center sd-text-dark +:class-body: sd-text-center +{fas}`users;fa-2x` Get Involved ^^^ -Coming Soon for Avogadro 2: +Help to make Avogadro better for everyone: -- [Getting Started](getting-started) -- [Manual](docs) -- [Tutorials](tutorials) +:::{button-ref} contrib +:color: primary +:shadow: +:align: center +Contribute +::: +:::{button-ref} Translate +:color: primary +:outline: +:align: center +Help with translation +::: +:::{button-link} https://github.com/OpenChemistry/avogadrolibs/issues/new?template=bug_report.md +:color: primary +:outline: +:align: center +Report a bug or issue +::: +:::{button-link} https://github.com/OpenChemistry/avogadrolibs/issues/new?template=feature_request.md +:color: primary +:outline: +:align: center +Request a feature ::: +:::: -:::{grid-item-card} -:class-header: sd-font-weight-bold sd-bg-light sd-text-center -{fas}`laptop-code;fa-2x` Develop -^^^ -Develop scripts and C++ code with Avogadro: +::::{grid-item-card} +:class-header: sd-font-weight-bold sd-bg-light sd-text-center sd-text-dark +:class-body: sd-text-center +{fas}`graduation-cap;fa-2x` Education +^^^ -- [Script Plugins](Scripts) -- Jupyter Notebooks -- [C++ API](develop) +Learn how Avogadro can be used in education: +:::{button-ref} teach +:color: primary +:shadow: +:align: center +Teach ::: -:::{grid-item-card} -:class-header: sd-font-weight-bold sd-bg-light sd-text-center -{fas}`users;fa-2x` Contribute +:::{button-ref} teaching-articles +:color: primary +:outline: +:align: center +Publications using Avogadro +::: +:::: + +::::{grid-item-card} +:class-header: sd-font-weight-bold sd-bg-light sd-text-center sd-text-dark +:class-body: sd-text-center +{fas}`comments;fa-2x` Community ^^^ -We want your help to make Avogadro better for everyone: +Ask questions, get feedback, and suggest ideas: -- Roadmap -- [Translation / Localization](Translate) -- [Bugs / Issues][issues] -- [Feature Requests][features] +:::{button-link} https://discuss.avogadro.cc/ +:color: primary +:shadow: +:align: center +Discuss +::: +:::{button-link} https://fosstodon.org/@avogadrochem +:color: primary +:outline: +:align: center +Follow on Mastodon +::: +:::{button-link} https://x.com/AvogadroChem +:color: primary +:outline: +:align: center +Follow on X +::: +:::{button-link} https://github.com/openchemistry/avogadrolibs/issues +:color: primary +:outline: +:align: center +GitHub project tracker ::: :::: -## Connecting with the Avogadro community -There are various ways to get in touch with the Avogadro community: +::::: -- [Avogadro Discussion] is the best place to ask questions and is a - great way to get feedback from other users on how to approach a problem, - suggest ideas, etc. -- If you think you've found a [bug][issues], or would like to request -a [feature][features], please report an issue on our [project tracker][tracker]. -- You can also find more information about Avogadro on [Twitter] or Mastodon. Feel free to - tag us on your papers and images! ```{toctree} :hidden: true