diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 97715a0..42ab86c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -15,13 +15,13 @@ jobs: steps: - uses: actions/checkout@v2 - - name: Set up Python 3.8 + - name: Set up Python 3.11 uses: actions/setup-python@v2 with: - python-version: '3.8' + python-version: '3.11' - name: Install python dependencies run: | pip install --upgrade pip pip install -rrequirements.txt - name: Run linkcheck - run: sphinx-build -b linkcheck docs/ docs/_build/linkcheck + run: sphinx-build -b linkcheck docs/ docs/_build/linkcheck --color -q diff --git a/create_post.py b/create_post.py index b7b7340..f3f1e55 100755 --- a/create_post.py +++ b/create_post.py @@ -13,6 +13,7 @@ "event": "Events", "report": "Reports", "release": "Releases", + "blog": "Blog", } diff --git a/docs/conf.py b/docs/conf.py index 628a617..6660048 100644 --- a/docs/conf.py +++ b/docs/conf.py @@ -17,6 +17,7 @@ "legacy_redirects", "check_events", "selective_css", + "sphinx_favicon", ] # see https://myst-parser.readthedocs.io @@ -29,6 +30,12 @@ templates_path = ["_templates"] html_show_sourcelink = False +# sphinx_favicon +favicons = [ + "favicon-16x16.png", + "favicon-32x32.png", +] + # see https://pydata-sphinx-theme.readthedocs.io html_theme_options = { # "announcement": "Welcome to the new AiiDA site!", @@ -36,18 +43,6 @@ "image_light": "logo-light.svg", "image_dark": "logo-dark.svg", }, - "favicons": [ - { - "rel": "icon", - "sizes": "16x16", - "href": "favicon-16x16.png", - }, - { - "rel": "icon", - "sizes": "32x32", - "href": "favicon-32x32.png", - }, - ], "icon_links": [ { "name": "Discourse", @@ -64,7 +59,7 @@ { "name": "Twitter", "url": "https://twitter.com/aiidateam", - "icon": "fa-brands fa-square-twitter", + "icon": "fa-brands fa-square-x-twitter", "type": "fontawesome", }, ], @@ -74,7 +69,7 @@ "theme-switcher", "navbar-icon-links", ], - "footer_items": ["copyright"], + "footer_start": ["copyright"], "use_edit_page_button": True, "search_bar_text": "Search ...", } @@ -148,6 +143,8 @@ r"https://aip.scitation.org/doi/.*", r"https://pubs.acs.org/doi/.*", r"https://www.sciencedirect.com/science/.*", + r"http://dx.doi.org/10.5075/epfl-thesis-7179", # EPFL blocks repeating requests + r"http://qe2019.ijs.si/index.html", # event page does not exist anymore ] aiida_ignore_event_checks = [ diff --git a/docs/events.yaml b/docs/events.yaml index 70d4b0e..8768b85 100644 --- a/docs/events.yaml +++ b/docs/events.yaml @@ -133,7 +133,6 @@ start: 2019-09-23 duration: 4 days location: SINTEF Oslo (NO) - url: https://www.sigma2.no/vasp-and-aiida-workshop-0 - name: AiiDA tutorial within the summer school on Advanced Materials and Molecular Modelling with Quantum ESPRESSO start: 2019-09-16 diff --git a/docs/news/posts/2020-05-27-new-mc-archive.md b/docs/news/posts/2020-05-27-new-mc-archive.md index 1b896e1..3c46821 100644 --- a/docs/news/posts/2020-05-27-new-mc-archive.md +++ b/docs/news/posts/2020-05-27-new-mc-archive.md @@ -11,7 +11,7 @@ We would like to announce the launch of a newly engineered [Materials Cloud Arch The [Materials Cloud Archive](https://archive.materialscloud.org/), active since March 2017, is a public, free, open-access repository for research data and tools in computational materials science and in related experimental efforts, inspired by the archive initiatives for preprints. It provides the capability to upload and persist arbitrary data records from anyone in the community with a minimum guaranteed 10-year retention time per record. Currently, 0.5 petabytes are already allocated; the  limits for standard submissions are of 5 GB for data sets in any format, and of 50 GB for AiiDA databases; moderators can approve larger data sets upon request. Each entry is assigned a globally unique and persistent digital object identifier (DOI) and harvestable metadata. The new Invenio platform makes it easier for authors to submit and later update data records, provides full-text searches, and powers streamlined workflows for content moderation. -The Archive is an integral part of the [Materials Cloud](https://www.materialscloud.org/) FAIR data infrastructure, in partnership with several European and national centres - these include the [MaX](http://www.max-centre.eu/) Centre of Excellence, the  [MARVEL](https://nccr-marvel.ch/) NCCR, the H2020 [MarketPlace](https://www.the-marketplace-project.eu/), [NFFA](http://www.nffa.eu/), and [Intersect](http://intersect-project.eu/) projects, [EMMC](https://emmc.eu/), [swissuniversities](https://www.materialscloud.org/swissuniversities), [PASC](https://www.pasc-ch.org/), and [OSSCAR](https://www.osscar.org/). It is a [recommended repository for Nature’s Scientific Data](https://www.nature.com/sdata/policies/repositories#materials), it is indexed by [FAIRsharing](https://fairsharing.org/biodbcore-001089/), [Google Dataset Search](https://datasetsearch.research.google.com/search?query=Materials%20Cloud) and [EOSC-hub](https://www.eosc-hub.eu/)/[EUDAT](https://www.eudat.eu/)’s service [B2FIND](http://b2find.eudat.eu/organization/materialscloud), and it is registered on [re3data](https://www.re3data.org/repository/r3d100012611). Finally, it is an official [implementation network](https://www.go-fair.org/implementation-networks/overview/materials-cloud/) of the [GO FAIR initiative](https://www.go-fair.org/). +The Archive is an integral part of the [Materials Cloud](https://www.materialscloud.org/) FAIR data infrastructure, in partnership with several European and national centres - these include the [MaX](http://www.max-centre.eu/) Centre of Excellence, the  [MARVEL](https://nccr-marvel.ch/) NCCR, the H2020 [MarketPlace](https://www.the-marketplace-project.eu/), [NFFA](http://www.nffa.eu/), and [Intersect](http://intersect-project.eu/) projects, [EMMC](https://emmc.eu/), [swissuniversities](https://www.materialscloud.org/swissuniversities), [PASC](https://www.pasc-ch.org/), and [OSSCAR](https://www.osscar.org/). It is a [recommended repository for Nature’s Scientific Data](https://www.nature.com/sdata/policies/repositories#materials), it is indexed by [FAIRsharing](https://fairsharing.org/biodbcore-001089/), [Google Dataset Search](https://datasetsearch.research.google.com/search?query=Materials%20Cloud) and [EOSC-hub](https://www.eosc-hub.eu/)/[EUDAT](https://www.eudat.eu/)’s service [B2FIND](http://b2find.eudat.eu/organization/materialscloud), and it is registered on [re3data](https://www.re3data.org/repository/r3d100012611). More information on the Materials Cloud integration of data, workflows and codes can be found in [L. Talirz et al., Materials Cloud, a platform for open computational science, arXiv:2003.12510 (2020)](https://arxiv.org/abs/2003.12510) and in [S. Huber et al., AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance, arXiv:2003.12476 (2020)](https://arxiv.org/abs/2003.12476). diff --git a/docs/news/posts/2021-03-28-aiida-160-release.md b/docs/news/posts/2021-03-28-aiida-160-release.md index 7de6a2e..21325d5 100644 --- a/docs/news/posts/2021-03-28-aiida-160-release.md +++ b/docs/news/posts/2021-03-28-aiida-160-release.md @@ -42,7 +42,7 @@ See the [Transferring data how-to](https://aiida.readthedocs.io/projects/aiida- The way the global/profile configuration is accessed has undergone a number of improvements: -* When loaded, the `config.json` (found in the `.aiida` folder) is now validated against a JSON Schema that can be found in [aiida/manage/configuration/schema](https://github.com/aiidateam/aiida-core/tree/develop/aiida/manage/configuration/schema). +* When loaded, the `config.json` (found in the `.aiida` folder) is now validated against a JSON Schema that can be found in [aiida/manage/configuration/schema](https://github.com/aiidateam/aiida-core/tree/v1.6.0/aiida/manage/configuration/schema). * The schema includes a number of new global/profile options, including: `transport.task_retry_initial_interval`, `transport.task_maximum_attempts`, `rmq.task_timeout` and `logging.aiopika_loglevel`. * The `cache_config.yml` has now also been **deprecated** and merged into the `config.json`, as part of the profile options. This merge will be handled automatically, upon first load of the `config.json` using the new AiiDA version. diff --git a/docs/news/posts/2021-10-06-coding-week-event.md b/docs/news/posts/2021-10-06-coding-week-event.md index de4d17e..286c5b2 100644 --- a/docs/news/posts/2021-10-06-coding-week-event.md +++ b/docs/news/posts/2021-10-06-coding-week-event.md @@ -178,7 +178,7 @@ We are very grateful to our sponsors for helping to make this event possible: - [EPFL](http://epfl.ch) for for providing administrative support - The [MARVEL National Centre of Competence in Research](http://nccr-marvel.ch/) “OSP” for funding - The [MaX European Centre of Excellence](http://www.max-centre.eu/) for funding -- The [swissuniversities P-5 project](https://www.swissuniversities.ch/en/organisation/projects-and-programmes/) “Materials Cloud” and [Empa](https://www.empa.ch/) for funding +- The [swissuniversities P-5 project](https://www.swissuniversities.ch/en/topics/digitalisation/p-5-scientific-information) “Materials Cloud” and [Empa](https://www.empa.ch/) for funding - The [MarketPlace](https://www.the-marketplace-project.eu/) project for funding - The [DOME](https://dome40.eu/) project for funding - The [Open-Model project](https://www.open-model.eu/) funding diff --git a/docs/news/posts/2022-11-24-ord-project-premise.md b/docs/news/posts/2022-11-24-ord-project-premise.md index 73f2b8f..16c020f 100644 --- a/docs/news/posts/2022-11-24-ord-project-premise.md +++ b/docs/news/posts/2022-11-24-ord-project-premise.md @@ -10,7 +10,7 @@ date: 2022-11-24 A consortium led by Dr. Giovanni Pizzi (project leader of [NCCR MARVEL's Pillar 3, "Digital Infrastructure of Open Simulations and Data,"](https://nccr-marvel.ch/research/iii/projects/open-digital-infrastructure) and Group leader of the ["Materials Software and Data" group](https://www.psi.ch/en/lms/msd-group) at the Paul Scherrer Institute PSI), including also researchers from Empa and ETH Zurich, has won funding of almost CHF1.3 million for a 3-year project funded under the ["ORD-R Establish" initiative of the ETH Board](https://ethrat.ch/en/measure-1-calls-for-field-specific-actions/). ## About the project -The project, dubbed PREMISE, aims to establish, promote and facilitate the adoption of Open Research Data (ORD) practices that adhere to FAIR data principles in the field of materials science. It will provide missing critical components to enable open and reproducible research, focusing in particular on the interoperability of data from simulations and experiments. +The project, dubbed [PREMISE](https://ord-premise.org/), aims to establish, promote and facilitate the adoption of Open Research Data (ORD) practices that adhere to FAIR data principles in the field of materials science. It will provide missing critical components to enable open and reproducible research, focusing in particular on the interoperability of data from simulations and experiments. During their project, the researchers will draw on the existing platforms [openBIS](https://openbis.ch/), an open-source data management platform developed at ETH Zurich, and [AiiDA](https://www.aiida.net), an open-source workflow management system mainly developed at PSI and EPFL. The two platforms focus on different parts of the data life cycle—experiments and simulations, respectively. You can read the [full press release here](https://nccr-marvel.ch/news/communication/11-PREMISE). diff --git a/docs/news/posts/2023-06-22-aiida-tightly-integr.md b/docs/news/posts/2023-06-22-aiida-tightly-integr.md index afd9e19..c780001 100644 --- a/docs/news/posts/2023-06-22-aiida-tightly-integr.md +++ b/docs/news/posts/2023-06-22-aiida-tightly-integr.md @@ -9,6 +9,6 @@ date: 2023-06-22 Microsoft recently launched their new [Azure Quantum Elements](https://quantum.microsoft.com/en-us/our-story/quantum-elements-overview) platform. We are happy to share that AiiDA is tightly integrated in it! -You can check out for instance the [launch video](https://news.microsoft.com/azure-quantum-june-event/#watch-now) introduced by Microsoft's CEO Satya Nadella (check e.g. from minute 13:00, where AiiDA workflows are used to drive workflows). +You can check out for instance the [launch video](https://news.microsoft.com/azure-quantum-june-event) introduced by Microsoft's CEO Satya Nadella (check e.g. from minute 13:00, where AiiDA workflows are used to drive workflows). If you are interested, you can also check out the [Microsoft webinar](https://connect.discoveracs.org/CENWebinar_Microsoft_6_22_23?partnerref=Microsoft) today at 5PM CEST, where they discuss their Azure Quantum platform to accelerate scientific discovery, and the interaction with AiiDA is also highlighted. diff --git a/docs/news/posts/2023-11-20-open-postdoc-position-marvel-2023.md b/docs/news/posts/2023-11-20-open-postdoc-position-marvel-2023.md new file mode 100644 index 0000000..61fd0c0 --- /dev/null +++ b/docs/news/posts/2023-11-20-open-postdoc-position-marvel-2023.md @@ -0,0 +1,24 @@ +--- +blogpost: true +category: News +tags: positions +date: 2023-11-20 +--- + +# 1 post-doc positions at PSI (Switzerland) on high-throughput materials discovery + +One new post-doc opportunity is open in the [Materials Software and Data Group](https://www.psi.ch/en/lms/msd-group) led by Dr. Giovanni Pizzi, part of the Laboratory for Materials Simulations, at the [Paul Scherrer Institute (PSI)](https://www.psi.ch/en), Switzerland. + +**The successful candidate will be in charge of setting up and maintaining large scale materials discovery projects based on the fully automated and robust computational infrastructure [AiiDA](https://www.aiida.net).** +Tasks will involve the management and coordination of scientific research projects (setting up the projects, writing the workflows, running the simulations, writing scientific papers), maintaining and documenting existing computational pipelines for generating the databases published on [Materials Cloud](https://www.materialscloud.org) (e.g., [MC3D](https://www.materialscloud.org/mc3d) and [MC2D](https://www.materialscloud.org/mc2d)), supporting the research community by maintaining and developing relevant plugins (e.g. AiiDA-Quantum ESPRESSO), and supporting the development of GUIs to new simulations via [AiiDAlab](https://www.aiidalab.net/). + +This positions is funded by the [NCCR MARVEL](https://nccr-marvel.ch/), offering close collaboration with project partners such as the Swiss Supercomputer Center CSCS, EPFL, and Empa, among others. Additionally, you will have the opportunity to network with current and former members of the well-established MARVEL community, with colleagues in the group and in the laboratory funded by other projects with strong synergies with MARVEL, and to engage in collaborative projects across Switzerland and Europe, expanding your network of international collaborations. + +We are seeking candidates with a PhD degree in the physical sciences (e.g., physics, chemistry, or materials science/engineering), strong organization skills, and a passion for writing open-source tools that can be used by a broad audience of researchers. +Essential qualifications include experience in running simulations on HPC and proficient software development and programming skills in Python. Desirable skills include experience in managing software projects in a team, handling large amounts of data, and developing complex automated computational tools for running simulations at scale. + +**More details and information, requirements for the positions, and instructions on how to apply can be found at ** + +**The application deadline is on December 10th, 2023.** + +If you know someone who might be interested in this opportunity, please feel free to forward this announcement to them. diff --git a/docs/news/posts/2023-12-20-release-2.5.0.md b/docs/news/posts/2023-12-20-release-2.5.0.md new file mode 100644 index 0000000..0c29ae4 --- /dev/null +++ b/docs/news/posts/2023-12-20-release-2.5.0.md @@ -0,0 +1,29 @@ +--- +blogpost: true +category: Releases +tags: aiida-core +date: 2023-12-20 +--- + +# AiiDA v2.5.0 released + +We are pleased to announce that AiiDA v2.5 was just released [^1]. +It can be installed as always from PyPI using pip: + + pip install aiida-core==2.5 + +or using Conda instead: + + conda install aiida-core=2.5 + +This release includes a number of interesting features and bug fixes. +For example, new storage backends are added that make it easy to setup profiles without a PostgreSQL server; ideal for testing and demonstration purposes. +For a complete overview, please refer to the change log [^2]. + +Happy computing! + +The AiiDA team + + +[^1]: https://pypi.org/project/aiida-core/2.5.0/ +[^2]: https://github.com/aiidateam/aiida-core/blob/v2.5.0/CHANGELOG.md diff --git a/docs/news/posts/2024-07-01-release-2.6.0.md b/docs/news/posts/2024-07-01-release-2.6.0.md new file mode 100644 index 0000000..9d4dc23 --- /dev/null +++ b/docs/news/posts/2024-07-01-release-2.6.0.md @@ -0,0 +1,18 @@ +--- +blogpost: true +category: Releases +tags: aiida-core +date: 2024-07-01 +--- + +# AiiDA v2.6.0 released + +We just released the latest version of AiiDA. This minor release comes with a number of features that are focused on user friendliness of the CLI and the API. The [changelog](https://aiida.readthedocs.io/projects/aiida-core/en/stable/reference/_changelog.html#v2-6-0-2024-07-01) contains a list of all changes including a nice overview of some of the new features. + +A lot of work has especially gone in making it easier to install AiiDA and try it out without having to install services like PostgreSQL and RabbitMQ. It is now possible to operate AiiDA without RabbitMQ, at the cost of losing daemon functionality. The new command `verdi presto` allows setting up a complete and ready-to-go profile with a single command without any configuration. The installation [documentation](https://aiida.readthedocs.io/projects/aiida-core/en/stable/installation/index.html) has seen a complete overhaul. + +The caching mechanism has received a number of improvements guaranteeing even greater savings of computational time. For existing calculations to be valid cache sources in the new version, their hash has to be regenerated (see [Improvements and changes to caching](https://aiida.readthedocs.io/projects/aiida-core/en/stable/reference/_changelog.html#improved-test-fixtures-without-services) for details). + +Happy computing! + +The AiiDA team diff --git a/docs/news/posts/2024-08-07-release-2.6.2.md b/docs/news/posts/2024-08-07-release-2.6.2.md new file mode 100644 index 0000000..f98e1bb --- /dev/null +++ b/docs/news/posts/2024-08-07-release-2.6.2.md @@ -0,0 +1,14 @@ +--- +blogpost: true +category: Releases +tags: aiida-core +date: 2024-08-07 +--- + +# AiiDA v2.6.2 released + +We just released the latest version of AiiDA, v2.6.2. This patch release comes with a number of bug fixes and additions to the documentation. You can find a list of all changes in the [changelog](https://github.com/aiidateam/aiida-core/blob/fb3686271fcdeb5506838a5a3069955546b05460/CHANGELOG.md). + +Happy computing! + +The AiiDA team diff --git a/docs/news/posts/2024-09-20-simpler-installation.md b/docs/news/posts/2024-09-20-simpler-installation.md new file mode 100644 index 0000000..fedf17b --- /dev/null +++ b/docs/news/posts/2024-09-20-simpler-installation.md @@ -0,0 +1,139 @@ +--- +blogpost: true +category: Blog +tags: usability +date: 2024-09-20 +--- + +# Simplifications to the installation of AiiDA since v2.0 + +Dear users, as we are always working hard to improve your experience with AiiDA, we would like to share with you some of +the new features aimed at user friendliness since the last major release v2.0. In this blog post, we will cover +improvements to the installation, so let's get started, shall we? + +## Service-less AiiDA + +_Get to a running AiiDA installation in seconds_ + +While `PostgreSQL` (PSQL) as database backend and `RabbitMQ` (RMQ) as message broker provide high-performance and +high-throughput capabilities, we have found over the years that their setup can pose an initial hurdle for new users. + +Therefore, recent changes have made it possible to run AiiDA entirely without them[^1]. This can be achieved with the +new command `verdi presto`, which reduces the installation effort of AiiDA to a mere two commands: + +```shell +pip install aiida-core +verdi presto +``` + +It only takes about 20 seconds, really: + +![From zero to AiiDA profile in 20 seconds](./_gifs/verdi-presto-white-10fps-2160p.gif) + +As you can see in the video above, on running `verdi presto`, you are greeted with: + +```shell +Report: Option `--use-postgres` not enabled: configuring the profile to use SQLite. +Report: RabbitMQ server not found (Failed to connect with following connection parameters: {'protocol': 'amqp', 'username': 'guest', 'password': 'guest', 'host': '127.0.0.1', 'port': 5672, 'virtual_host': ''}): configuring the profile without a broker. +Report: See https://aiida-core.readthedocs.io/en/stable/installation/guide_quick.html#quick-install-limitations for details on the limitations of running without a broker. +Report: Initialising the storage backend. +Report: Storage initialisation completed. +Success: Created new profile `presto`. +Success: Configured the localhost as a computer. +``` + +And after successfull profile creation, `verdi status` returns something like: + +```shell + ✔ version: AiiDA v2.6.2 + ✔ config: /home/geiger_j/aiida_projects/aiida-website/.aiida + ✔ profile: presto + ✔ storage: SqliteDosStorage[/home/geiger_j/aiida_projects/aiida-website/.aiida/repository/sqlite_dos_d2a4e83ea09141678de8ea4b2250fc69]: open, + ⏺ broker: No broker defined for this profile: certain functionality not available. + ⏺ daemon: No broker defined for this profile: daemon is not available. +``` + +`verdi presto`, by default, uses SQLite instead of PSQL, however, the latter can also be selected with +the `--use-postgres` flag. + +In addition, the command works without RMQ, creating a profile without a +[broker](https://aiida.readthedocs.io/projects/aiida-core/en/v2.6.2/topics/processes/usage.html#manipulating-processes) +and [daemon](https://aiida.readthedocs.io/projects/aiida-core/en/v2.6.2/topics/daemon.html#daemon). If, instead, RMQ was +already available on the system[^2], it is automatically set up for your AiiDA profile, and the output of `verdi presto` +will be slightly different. + +```shell +Report: Option `--use-postgres` not enabled: configuring the profile to use SQLite. +Report: RabbitMQ server detected: configuring the profile with a broker. +Report: Initialising the storage backend. +Report: Storage initialisation completed. +Success: Created new profile `presto`. +Success: Configured the localhost as a computer. +``` + +Now, assume you initially created your profile without RMQ, but would then like to upgrade: Worry not, you can still +configure it after profile creation, using: + +```shell +verdi profile configure-rabbitmq +``` + +You can see the full process right here: + +![Upgrade profile with RMQ down the road](./_gifs/configure-rabbitmq-white-10fps-2160p.gif) + +## New way to manually create a profile + +`verdi presto` serves as a fully automated shortcut to create a profile. If you desire more fine-grained control, +e.g. over the database backend, you can also use the new command: + +```shell +verdi profile setup +``` + +When run as shown above, the different storage backends will be listed[^3]. + +For instance, to set up a profile with SQLite, the command could be: + +```shell +verdi profile setup core.sqlite_dos --profile-name aiida_rocks --email aiida_rocks@mail.com +``` + +Upon execution, you will be asked for the remaining options interactively: + +![Create a profile with `verdi profile setup`](./_gifs/verdi-profile-setup-white-10fps-2160p.gif) + +Lastly, please note that the previous commands `verdi setup` and `verdi quicksetup` still work for now, but deprecation +warnings will be issued as we eventually plan to remove them. + +**Have fun getting your feet wet! 🚀** + +--- + +**Relevant PRs** + +For the more tech-savvy among us, here are the most relevant PRs with the changes outlined in this blog post: + +- [[#6023]](https://github.com/aiidateam/aiida-core/pull/6023) Add `verdi profile setup` +- [[#6148]](https://github.com/aiidateam/aiida-core/pull/6148) Add the `SqliteDosStorage` storage backend +- [[#6454]](https://github.com/aiidateam/aiida-core/pull/6454) CLI: Add the `verdi profile configure-rabbitmq` command + +**Footnotes** + +[^1]: + It should be kept in mind, however, that these two changes come at the cost of lower performance, and should, at + least for now, not be used in production (we are currently working on reducing possible limitations as much as + possible). Rather, they are mainly intended for new users to get a running AiiDA instance quickly and be able to + play around with the tool. The absence of the broker and daemon does not allow *submitting* of jobs, but only + *running* them in a blocking manner (remote execution, e.g. on HPC resources, is still possible, though), and SQLite + can handle concurrent writes to the database worse than PSQL. + +[^2]: + Installation should be fairly simple, e.g. via `sudo apt install rabbitmq-server` on Ubuntu. + +[^3]: + The [complete installation + guide](https://aiida.readthedocs.io/projects/aiida-core/en/v2.6.2/installation/guide_complete.html) provides a + concise overview of the simplified installation process using `verdi profile setup`. We also added a [dedicated + section](https://aiida.readthedocs.io/projects/aiida-core/en/v2.6.2/topics/storage.html) to the + documentation that gives an overview of the available database backends, and recommendations when to use which. diff --git a/docs/news/posts/2024-10-04-data-access.md b/docs/news/posts/2024-10-04-data-access.md new file mode 100644 index 0000000..cdd83a6 --- /dev/null +++ b/docs/news/posts/2024-10-04-data-access.md @@ -0,0 +1,253 @@ +--- +blogpost: true +category: Blog +tags: usability +date: 2024-10-04 +--- + +# Improvements in the ways to get your data out of AiiDA + +Dear users, as the saying goes "Data is the Gold of the 21st Century", in today's blog post, we would like to showcase +improvements in how you can get your data out of AiiDA's internal storage. We hope that these new features will enrich +not only you, but also the science you conduct. + +## Dumping process data to disk + +_From AiiDA's internal storage to classical directory trees_ + +As you might be aware, AiiDA uses an SQL +[database](https://aiida.readthedocs.io/projects/aiida-core/en/v2.6.2/topics/storage.html), as well as an internal [file +repository](https://aiida.readthedocs.io/projects/aiida-core/en/stable/topics/repository.html#repository) [^1] to store +your data locally [^2]. Both are optimized towards high performance and therefore constructed to be machine-readable +rather than human-readable. Hence, the difference between AiiDA's internal data storage and the typical file-system +approach (that most of us are familiar with) can make it cumbersome to get your data out of AiiDA onto your file system +in an easily understandable form. + +Therefore, you, the user, are effectively forced to use the `verdi` CLI interface or AiiDA's Python API (e.g. the +`QueryBuilder` class) to access your data, making the transition towards AiiDA more challenging. To ease this +transition, we have [added +functionality](https://aiida.readthedocs.io/projects/aiida-core/en/v2.6.2/howto/data.html#dumping-data-to-disk) to dump +AiiDA `Process` data to disk in an intuitive directory structure via: + +```shell +verdi process dump +``` + +The following video shows the result of running the command for a `PwCalculation` that was used to execute the `pw.x` +executable of Quantum ESPRESSO: + +![PwCalculation dump](./_gifs/calculation-dump-white-10fps-2160p.gif) + +And for a more complex `PwBandsWorkChain` (which actually contains the previously shown `PwCalculation` as one of its steps): + +![PwBandsWorkChain dump](./_gifs/workflow-dump-white-10fps-2160p.gif) + +As you can see, the command works both for individual calculations and for nested workflows, resulting in +the following output directories [^3]. + +**`tree` on a dumped example `CalcJob`:** + +```shell +dump-PwCalculation-54 +├── README.md +├── inputs +│ ├── _aiidasubmit.sh +│ └── aiida.in +├── outputs +│ ├── _scheduler-stderr.txt +│ ├── _scheduler-stdout.txt +│ ├── aiida.out +│ └── data-file-schema.xml +└── node_inputs + └── pseudos + └── Si + └── Si.pbesol-n-rrkjus_psl.1.0.0.UPF +``` + +**`tree -d` on a dumped example `WorkChain`:** + +```shell +dump-PwBandsWorkChain-70 +├── 01-relax-PwRelaxWorkChain +│ ├── 01-iteration_01-PwBaseWorkChain +│ │ ├── 01-create_kpoints_from_distance +│ │ │ └── inputs +│ │ └── 02-iteration_01-PwCalculation +│ │ ├── inputs +│ │ ├── node_inputs +│ │ │ └── pseudos +│ │ │ └── Si +│ │ └── outputs +│ └── 02-iteration_02-PwBaseWorkChain +│ ├── 01-create_kpoints_from_distance +│ │ └── inputs +│ └── 02-iteration_01-PwCalculation +│ ├── inputs +│ ├── node_inputs +│ │ └── pseudos +│ │ └── Si +│ └── outputs +├── 02-seekpath-seekpath_structure_analysis +│ └── inputs +├── 03-scf-PwBaseWorkChain +│ ├── ... +... +``` + +Therefore, after running the command once, you'll have all data involved in the execution of your workflow directly +accessible as a standard folder [^4]. This allows you to explore it with your favorite file explorer or command-line +tool. + +Happy grepping! + +## New QueryBuilder Syntax + +_SQL queries, but intuitive!_ + +In addition to accessing raw files as outlined above, AiiDA's powerful SQL database allows querying for stored nodes, +which can be achieved with the `QueryBuilder` class (as documented +[here](https://aiida.readthedocs.io/projects/aiida-core/en/v2.6.2/howto/query.html)). While using the `QueryBuilder` is +(at least for most of us) easier than writing raw SQL queries, its syntax typically requires some familiarization [^5]. + +Recent improvements have therefore enabled an alternative, more intuitive way to construct queries. Let us explain with +the following example: Assume you wanted to obtain all integers with values in a range between 1 and 10 (both excluded) +from a `Group` called "integers", and return their respective PKs and values. To achieve this, you'd have to construct +the following, rather convoluted query: + +```python +from aiida import orm + +qb = orm.QueryBuilder() +qb.append( + orm.Group, + filters={ + "label": "integers", + }, + project=["label"], + tag="group", +) +qb.append( + orm.Int, + with_group="group", + filters={ + "and": [ + {"attributes.value": {">": 1}}, + {"attributes.value": {"<": 10}}, + ] + }, + project=["pk", "attributes.value"], +) +``` + +In the code snippet above, we first import AiiDA's [object-relational +mapping](https://en.wikipedia.org/wiki/Object%E2%80%93relational_mapping) (`orm`) module, and then instantiate the +`QueryBuilder` class. The query is then gradually built up by adding the desired specifications using the `append` +method. Here, we first apply filtering for groups that are labelled "integers" and tag this filter as "group" so that we +can link it with the second `append`. In this second call of the method, we only filter for integers of AiiDA's integer +data type (`orm.Int`) that are part of our previously defined group via `with_group="group"`. We then apply the filter +that the values of the integers should be in our desired range between 1 and 10, and, lastly, using +`project=["pk", "attributes.value"]`, we only return the primary keys and actual values of the AiiDA `orm.Int` nodes we +obtain from our query (rather than, say, the entire AiiDA `Node` instance). + +Instead, the new QueryBuilder syntax allows accessing attributes of AiiDA nodes via the [new `fields` +specifier](https://aiida.readthedocs.io/projects/aiida-core/en/v2.6.2/reference/_changelog.html#programmatic-syntax-for-query-builder-filters-and-projections), +with which the filtering logic can be applied to them directly: + +```python +from aiida import orm + +qb = orm.QueryBuilder() +qb.append( + orm.Group, + filters=orm.Group.fields.label == "integers", + project=[orm.Group.fields.label], + tag="group", +) +qb.append( + orm.Int, + with_group="group", + filters=(orm.Int.fields.value > 1) & (orm.Int.fields.value < 10), + project=[orm.Int.fields.pk, orm.Int.fields.value], +) +``` + +Hence, for example the filter on the values of the integer nodes reduces from: + +```python +filters={ + "and": [ + {"attributes.value": {">": 1}}, + {"attributes.value": {"<": 10}}, + ] +} +``` + +to the more concise: + +```python +filters=(orm.Int.fields.value > 1) & (orm.Int.fields.value < 10), +``` + +in which the `"and"` condition can be expressed via the ampersand (`&`) and directly be applied on the relevant +entities. Furthermore, accessing through the `.fields` attribute, e.g. in the updated `project` specifier: + +```python +project=[orm.Int.fields.pk, orm.Int.fields.value] +``` + +albeit being slightly more verbose, is less prone to errors than access via string identifiers in the previous version: + +```python +project=["pk", "attributes.value"] +``` + +as it allows for autocompletion. + +Any feedback on the new QueryBuilder syntax welcome! + +*** + +## Relevant PRs + +For the more tech-savvy among us, here are the relevant PRs of the changes outlined in this blog post: + +- [[#6276]](https://github.com/aiidateam/aiida-core/pull/6276) Add CLI command to dump inputs/outputs of `CalcJob`/`WorkChain` +- [[#6245]](https://github.com/aiidateam/aiida-core/pull/6245) ✨ NEW: Add `orm.Entity.fields` interface for `QueryBuilder` + (cont.) [and linked PRs] + +## Footnotes + +[^1]: + The file repository is based on the [`disk-objectstore`](https://github.com/aiidateam/disk-objectstore) + implementation. If you ever wondered what the `_dos` appendix of the `core.psql_dos` and `core.sqlite_dos` storage + backends means, now you know! 😉 + +[^2]: + The discussion in the main text of this blog post refers to the files and data stored by AiiDA on the local computer + where AiiDA is installed, and which are preserved long-term in its internal file repository. These files are + obtained, e.g. by retrieval from the _remote_ computer once a calculation finishes, or could be parsed data or + inputs provided by the user. Instead, during the execution of your calculations _on the remote computer_, files are + located in a subfolder of the `work_directory` of the used `Computer` (typically in the `scratch`), where the + subfolder name is generated from the UUID of the AiiDA `CalculationNode`. This directory has a three-level depth, + obtained by "sharding" the UUID based on the first characters. For istance, if the UUID is + `6861d8fb-4694-46be-b0e6-7282989f069d`, the calculation will run in a subfolder named + `68/61/d8fb-4694-46be-b0e6-7282989f069d`. + +[^3]: + The workflow is recursively traversed, and files are written to disk for each calculation (remember, it's the + `Calculation` that actually creates the data, while the `Workflow` can only return it, as [outlined + here](https://aiida.readthedocs.io/projects/aiida-core/en/v2.6.2/topics/processes/concepts.html#process-types)). In + the `verdi process dump` feature, the subdirectory naming is automatically determined based on the iteration + counter, the link label, and the class name, leading to a directory structure that mirrors the execution logic of + the workflow. + +[^4]: + The `verdi process dump` feature is currently still actively developed to enable obtaining remote and stashed data + entities, e.g., intermediate files of the workflow that weren't originally retrieved from the remote + (high-performance) computer or data that was moved to tape. In addition, we are working on allowing to `dump` larger + collections of data, such as groups, or even all data contained in an AiiDA profile, again, in an easily + understandable folder structure. So stay tuned! + +[^5]: + Modern LLMs like ChatGPT and Claude can actually generate (somewhat correct) AiiDA `QueryBuilder` queries (at least + with the syntax until their training data cutoff date), so they can provide a good starting point for your queries. diff --git a/docs/news/posts/_gifs/calculation-dump-white-10fps-2160p.gif b/docs/news/posts/_gifs/calculation-dump-white-10fps-2160p.gif new file mode 100644 index 0000000..2d85dcb Binary files /dev/null and b/docs/news/posts/_gifs/calculation-dump-white-10fps-2160p.gif differ diff --git a/docs/news/posts/_gifs/configure-rabbitmq-white-10fps-2160p.gif b/docs/news/posts/_gifs/configure-rabbitmq-white-10fps-2160p.gif new file mode 100644 index 0000000..f608f01 Binary files /dev/null and b/docs/news/posts/_gifs/configure-rabbitmq-white-10fps-2160p.gif differ diff --git a/docs/news/posts/_gifs/verdi-presto-white-10fps-2160p.gif b/docs/news/posts/_gifs/verdi-presto-white-10fps-2160p.gif new file mode 100644 index 0000000..fcdaef5 Binary files /dev/null and b/docs/news/posts/_gifs/verdi-presto-white-10fps-2160p.gif differ diff --git a/docs/news/posts/_gifs/verdi-profile-setup-white-10fps-2160p.gif b/docs/news/posts/_gifs/verdi-profile-setup-white-10fps-2160p.gif new file mode 100644 index 0000000..e4fc73e Binary files /dev/null and b/docs/news/posts/_gifs/verdi-profile-setup-white-10fps-2160p.gif differ diff --git a/docs/news/posts/_gifs/workflow-dump-white-10fps-2160p.gif b/docs/news/posts/_gifs/workflow-dump-white-10fps-2160p.gif new file mode 100644 index 0000000..7ea8ae0 Binary files /dev/null and b/docs/news/posts/_gifs/workflow-dump-white-10fps-2160p.gif differ diff --git a/docs/pics/sponsors/placeholder-logo-300x150.png b/docs/pics/sponsors/placeholder-logo-300x150.png new file mode 100644 index 0000000..a353039 Binary files /dev/null and b/docs/pics/sponsors/placeholder-logo-300x150.png differ diff --git a/docs/pics/sponsors/premise-logo-300x150.png b/docs/pics/sponsors/premise-logo-300x150.png new file mode 100644 index 0000000..8819daf Binary files /dev/null and b/docs/pics/sponsors/premise-logo-300x150.png differ diff --git a/docs/sections/acknowledgements.md b/docs/sections/acknowledgements.md index aa3fc27..8c65f85 100644 --- a/docs/sections/acknowledgements.md +++ b/docs/sections/acknowledgements.md @@ -6,7 +6,8 @@ AiiDA development is supported or has been supported by: * - ![logo](../pics/sponsors/marvel-logo-300x150.png) - [NCCR MARVEL](https://nccr-marvel.ch/)\ - *MARVEL National Centre for Competence in Research* + *MARVEL National Centre for Competence in Research*\ + *funded by [SNSF](https://www.snf.ch/)* * - ![logo](../pics/sponsors/max-logo-300x150.png) - [MaX CoE](http://www.max-centre.eu/)\ @@ -48,4 +49,13 @@ AiiDA development is supported or has been supported by: - [Bosch](https://www.bosch.com/research/)\ *Bosch Research and Technology Center (USA)* +* - ![logo](../pics/sponsors/premise-logo-300x150.png) + - [ORD-PREMISE](https://www.ord-premise.org/)\ + *Open and Reproducible Materials Science Research*\ + *funded by the [ETH Board](https://ethrat.ch/en/)* + +* - ![logo](../pics/sponsors/placeholder-logo-300x150.png) + - [SwissTwins](https://www.bosch.com/research/)\ + *funded by the Swiss State Secretariat for Education, Research and Innovation (SERI)* + ::: diff --git a/docs/sections/science.md b/docs/sections/science.md index 925088b..42f7a33 100644 --- a/docs/sections/science.md +++ b/docs/sections/science.md @@ -10,16 +10,90 @@ The AiiDA team conducts an **annual survey** on the [AiiDA mailing list](./maili ## AiiDA-powered publications :::{figure} ../pics/publication-chart.png -A list of publications containing calculations powered by AiiDA, selected from the [citations of the AiiDA paper](https://scholar.google.com/scholar?cites=10268089832296963062&as_sdt=2005&sciodt=0,5&hl=en). +A histogram of publications containing calculations powered by AiiDA, selected from the [citations of the AiiDA paper](https://scholar.google.com/scholar?cites=10268089832296963062&as_sdt=2005&sciodt=0,5&hl=en). ::: +If you use AiiDA in your research and your paper is not listed on this page, feel free to send us an [email](mailto:developers@aiida.net) with the DOI of your paper. + + +### Publications* from 2024 (up to March) +_* This is an incomplete list of research papers that utilise AiiDA. Extracted manually from all citations of just these two articles ([Main](https://doi.org/10.1038/s41597-020-00638-4) and [Engine](https://doi.org/10.1016/j.commatsci.2020.110086))_ + +- Y. Wang, Y. Li, Z. Tang, H. Li, Z. Yuan, H. Tao, N. Zou, T. Bao, X. Liang, Z. Chen, S. Xu, C. Bian, Z. Xu, C. Wang, C. Si, W. Duan, Y. Xu, [Universal materials model of deep-learning density functional theory Hamiltonian](https://doi.org/10.1016/j.scib.2024.06.011), _Science Bulletin_, *pre-proofs* (2024). +- H. Saßnick, F. Machado Ferreira De Araujo, J. Edzards, C. Cocchi, [Impact of Ligand Substitution and Metal Node Exchange in the Electronic Properties of Scandium Terephthalate Frameworks](https://doi.org/10.1021/acs.inorgchem.3c03945), _Inorganic Chemistry_ **63,** 2098-2108 (2024). +- A. Tellez-Mora, X. He, E. Bousquet, L. Wirtz, A. Romero, [Systematic determination of a material’s magnetic ground state from first principles](https://doi.org/10.1038/s41524-024-01202-z), _npj Computational Materials_ **10,** no. 20, (2024). +- D. Grassano, N. Marzari, D. Campi, [High-throughput screening of Weyl semimetals](https://doi.org/10.1103/physrevmaterials.8.024201), _Physical Review Materials_ **8,** no. 024201, (2024). +- H. Saßnick, C. Cocchi, [Automated analysis of surface facets: the example of cesium telluride](https://doi.org/10.1038/s41524-024-01224-7), _npj Computational Materials_ **10,** no. 38, (2024). + + +### Publications* from 2023 +_* This is an incomplete list of research papers that utilise AiiDA. Extracted manually from all citations of just these two articles ([Main](https://doi.org/10.1038/s41597-020-00638-4) and [Engine](https://doi.org/10.1016/j.commatsci.2020.110086))_ + +- K. Jablonka, A. Rosen, A. Krishnapriyan, B. Smit, [An Ecosystem for Digital Reticular Chemistry](https://doi.org/10.1021/acscentsci.2c01177), _ACS Central Science_ **9,** 563-581 (2023). +- F. dos Santos, N. Marzari, [Fermi energy determination for advanced smearing techniques](https://doi.org/10.1103/physrevb.107.195122), _Physical Review B_ **107,** no. 195122, (2023). +- M. Bonacci, J. Qiao, N. Spallanzani, A. Marrazzo, G. Pizzi, E. Molinari, D. Varsano, A. Ferretti, D. Prezzi, [Towards high-throughput many-body perturbation theory: efficient algorithms and automated workflows](https://doi.org/10.1038/s41524-023-01027-2), _npj Computational Materials_ **9,** no. 74, (2023). +- B. Mourino, K. Jablonka, A. Ortega‐Guerrero, B. Smit, [In Search of Covalent Organic Framework Photocatalysts: A DFT‐Based Screening Approach](https://doi.org/10.1002/adfm.202301594), _Advanced Functional Materials_ **33,** (2023). +- S. Shepherd, G. Tribello, D. Wilkins, [A fully quantum-mechanical treatment for kaolinite](https://doi.org/10.1063/5.0152361), _The Journal of Chemical Physics_ **158,** (2023). +- S. Muy, C. Johnston, N. Marzari, [AiiDA-defects: an automated and fully reproducible workflow for the complete characterization of defect chemistry in functional materials](https://doi.org/10.1088/2516-1075/ace014), _Electronic Structure_ **5,** 024009 (2023). +- D. Campi, N. Mounet, M. Gibertini, G. Pizzi, N. Marzari, [Expansion of the Materials Cloud 2D Database](https://doi.org/10.1021/acsnano.2c11510), _ACS Nano_ **17,** 11268-11278 (2023). +- D. Li, H. Wang, K. Li, B. Zhu, K. Jiang, D. Backes, L. Veiga, J. Shi, P. Roy, M. Xiao, A. Chen, Q. Jia, T. Lee, S. Dhesi, D. Scanlon, J. MacManus-Driscoll, P. van Aken, K. Zhang, W. Li, [Emergent and robust ferromagnetic-insulating state in highly strained ferroelastic LaCoO3 thin films](https://doi.org/10.1038/s41467-023-39369-6), _Nature Communications_ **14,** no. 3638, (2023). +- S. Ghosh, P. Rüßmann, Y. Mokrousov, F. Freimuth, A. Kosma, [Perspective on spin–orbit torque, topology, and reciprocal and real-space spin textures in magnetic materials and heterostructures](https://doi.org/10.1063/5.0149849), _Journal of Applied Physics_ **133,** (2023). +- J. Cen, B. Zhu, D. Scanlon, [Exploring battery cathode materials in the Li-Ni-O phase diagrams using structure prediction](https://doi.org/10.1088/2515-7655/acdd9c), _Journal of Physics: Energy_ **5,** 035005 (2023). +- F. Yao, V. Multian, Z. Wang, N. Ubrig, J. Teyssier, F. Wu, E. Giannini, M. Gibertini, I. Gutiérrez-Lezama, A. Morpurgo, [Multiple antiferromagnetic phases and magnetic anisotropy in exfoliated CrBr3 multilayers](https://doi.org/10.1038/s41467-023-40723-x), _Nature Communications_ **14,** no. 4969, (2023). +- J. Železný, Y. Yahagi, C. Gomez-Olivella, Y. Zhang, Y. Sun, [High-throughput study of the anomalous Hall effect](https://doi.org/10.1038/s41524-023-01113-5), _npj Computational Materials_ **9,** no. 151, (2023). +- M. Vogler, J. Busk, H. Hajiyani, P. Jørgensen, N. Safaei, I. Castelli, F. Ramirez, J. Carlsson, G. Pizzi, S. Clark, F. Hanke, A. Bhowmik, H. Stein, [Brokering between tenants for an international materials acceleration platform](https://doi.org/10.1016/j.matt.2023.07.016), _Matter_ **6,** 2647-2665 (2023). +- D. Grassano, D. Campi, A. Marrazzo, N. Marzari, [Complementary screening for quantum spin Hall insulators in two-dimensional exfoliable materials](https://doi.org/10.1103/physrevmaterials.7.094202), _Physical Review Materials_ **7,** no. 094202, (2023). +- L. Ghiringhelli, C. Baldauf, T. Bereau, S. Brockhauser, C. Carbogno, J. Chamanara, S. Cozzini, S. Curtarolo, C. Draxl, S. Dwaraknath, Á. Fekete, J. Kermode, C. Koch, M. Kühbach, A. Ladines, P. Lambrix, M. Himmer, S. Levchenko, M. Oliveira, A. Michalchuk, R. Miller, B. Onat, P. Pavone, G. Pizzi, B. Regler, G. Rignanese, J. Schaarschmidt, M. Scheidgen, A. Schneidewind, T. Sheveleva, C. Su, D. Usvyat, O. Valsson, C. Wöll, M. Scheffler, [Shared metadata for data-centric materials science](https://doi.org/10.1038/s41597-023-02501-8), _Scientific Data_ **10,** no. 626, (2023). +- P. Henkel, J. Li, G. Grandhi, P. Vivo, P. Rinke, [Screening Mixed-Metal Sn2M(III)Ch2X3 Chalcohalides for Photovoltaic Applications](https://doi.org/10.1021/acs.chemmater.3c01629), _Chemistry of Materials_ **35,** 7761-7769 (2023). +- J. Qiao, G. Pizzi, N. Marzari, [Automated mixing of maximally localized Wannier functions into target manifolds](https://doi.org/10.1038/s41524-023-01147-9), _npj Computational Materials_ **9,** no. 206, (2023). +- Q. Chen, M. Di Giovannantonio, K. Eimre, J. Urgel, P. Ruffieux, C. Pignedoli, K. Müllen, R. Fasel, A. Narita, [On‐Surface Interchain Coupling and Skeletal Rearrangement of Indenofluorene Polymers](https://doi.org/10.1002/macp.202300345), _Macromolecular Chemistry and Physics_ **224,** (2023). +- E. Bosoni, L. Beal, M. Bercx, P. Blaha, S. Blügel, J. Bröder, M. Callsen, S. Cottenier, A. Degomme, V. Dikan, K. Eimre, E. Flage-Larsen, M. Fornari, A. Garcia, L. Genovese, M. Giantomassi, S. Huber, H. Janssen, G. Kastlunger, M. Krack, G. Kresse, T. Kühne, K. Lejaeghere, G. Madsen, M. Marsman, N. Marzari, G. Michalicek, H. Mirhosseini, T. Müller, G. Petretto, C. Pickard, S. Poncé, G. Rignanese, O. Rubel, T. Ruh, M. Sluydts, D. Vanpoucke, S. Vijay, M. Wolloch, D. Wortmann, A. Yakutovich, J. Yu, A. Zadoks, B. Zhu, G. Pizzi, [How to verify the precision of density-functional-theory implementations via reproducible and universal workflows](https://doi.org/10.1038/s42254-023-00655-3), _Nature Reviews Physics_ **6,** 45-58 (2023). +- P. Rüßmann, M. Bahari, S. Blügel, B. Trauzettel, [Interorbital Cooper pairing at finite energies in Rashba surface states](https://doi.org/10.1103/physrevresearch.5.043181), _Physical Review Research_ **5,** no. 043181, (2023). +- Q. Yang, I. Surin, J. Geiger, H. Eliasson, M. Agrachev, V. Kondratenko, A. Zanina, F. Krumeich, G. Jeschke, R. Erni, E. Kondratenko, N. López, J. Pérez-Ramírez, [Lattice-Stabilized Chromium Atoms on Ceria for N2O Synthesis](https://doi.org/10.1021/acscatal.3c04463), _ACS Catalysis_ **13,** 15977-15990 (2023). +- P. Si, A. Jayanth, O. Andreussi, [Soft‐sphere continuum solvation models for nonaqueous solvents](https://doi.org/10.1002/jcc.27254), _Journal of Computational Chemistry_ **45,** 719-737 (2023). +- X. Wei, A. Jalil, P. Rüßmann, Y. Ando, D. Grützmacher, S. Blügel, J. Mayer, [Atomic Diffusion-Induced Polarization and Superconductivity in Topological Insulator-Based Heterostructures](https://doi.org/10.1021/acsnano.3c08601), _ACS Nano_ **18,** 571-580 (2023). +- G. Gebreyesus, L. Bastonero, M. Kotiuga, N. Marzari, I. Timrov, [Understanding the role of Hubbard corrections in the rhombohedral phase of BaTiO3](https://doi.org/10.1103/physrevb.108.235171), _Physical Review B_ **108,** no. 235171, (2023). + + +### Publications* from 2022 +_* This is an incomplete list of research papers that utilise AiiDA. Extracted manually from all citations of just these two articles ([Main](https://doi.org/10.1038/s41597-020-00638-4) and [Engine](https://doi.org/10.1016/j.commatsci.2020.110086))_ + +- M. Schmitt, T. Denneulin, A. Kovács, T. Saunderson, P. Rüßmann, A. Shahee, T. Scholz, A. Tavabi, M. Gradhand, P. Mavropoulos, B. Lotsch, R. Dunin-Borkowski, Y. Mokrousov, S. Blügel, M. Kläui, [Skyrmionic spin structures in layered Fe5GeTe2 up to room temperature](https://doi.org/10.1038/s42005-022-01031-w), _Communications Physics_ **5,** no. 254, (2022). +- L. Gigli, M. Veit, M. Kotiuga, G. Pizzi, N. Marzari, M. Ceriotti, [Thermodynamics and dielectric response of BaTiO3 by data-driven modeling](https://doi.org/10.1038/s41524-022-00845-0), _npj Computational Materials_ **8,** no. 209, (2022). +- V. Borisov, Q. Xu, N. Ntallis, R. Clulow, V. Shtender, J. Cedervall, M. Sahlberg, K. Wikfeldt, D. Thonig, M. Pereiro, A. Bergman, A. Delin, O. Eriksson, [Tuning skyrmions in B20 compounds by 4d and 5d doping](https://doi.org/10.1103/physrevmaterials.6.084401), _Physical Review Materials_ **6,** no. 084401, (2022). +- T. Hsu, T. Pham, N. Keilbart, S. Weitzner, J. Chapman, P. Xiao, S. Qiu, X. Chen, B. Wood, [Efficient and interpretable graph network representation for angle-dependent properties applied to optical spectroscopy](https://doi.org/10.1038/s41524-022-00841-4), _npj Computational Materials_ **8,** no. 151, (2022). +- W. Xu, K. Reuter, M. Andersen, [Predicting binding motifs of complex adsorbates using machine learning with a physics-inspired graph representation](https://doi.org/10.1038/s43588-022-00280-7), _Nature Computational Science_ **2,** 443-450 (2022). +- S. Vijay, G. Kastlunger, K. Chan, J. Nørskov, [Limits to scaling relations between adsorption energies?](https://doi.org/10.1063/5.0096625), _The Journal of Chemical Physics_ **156,** (2022). +- D. Marchand, W. Curtin, [Machine learning for metallurgy IV: A neural network potential for Al-Cu-Mg and Al-Cu-Mg-Zn](https://doi.org/10.1103/physrevmaterials.6.053803), _Physical Review Materials_ **6,** no. 053803, (2022). +- A. Lund, G. Manohara, A. Song, K. Jablonka, C. Ireland, L. Cheah, B. Smit, S. Garcia, J. Reimer, [Characterization of Chemisorbed Species and Active Adsorption Sites in Mg–Al Mixed Metal Oxides for High-Temperature CO2 Capture](https://doi.org/10.1021/acs.chemmater.1c03101), _Chemistry of Materials_ **34,** 3893-3901 (2022). +- D. Li, B. Zhu, D. Backes, L. Veiga, T. Lee, H. Wang, Q. He, P. Roy, J. Zhang, J. Shi, A. Chen, P. van Aken, Q. Jia, S. Dhesi, D. Scanlon, K. Zhang, W. Li, [Manipulating the metal-to-insulator transition and magnetic properties in manganite thin films via epitaxial strain](https://doi.org/10.1103/physrevb.105.165426), _Physical Review B_ **105,** no. 165426, (2022). +- M. Betti, E. Placidi, C. Izzo, E. Blundo, A. Polimeni, M. Sbroscia, J. Avila, P. Dudin, K. Hu, Y. Ito, D. Prezzi, M. Bonacci, E. Molinari, C. Mariani, [Gap Opening in Double-Sided Highly Hydrogenated Free-Standing Graphene](https://doi.org/10.1021/acs.nanolett.2c00162), _Nano Letters_ **22,** 2971-2977 (2022). +- H. Yang, N. Bansal, P. Rüßmann, M. Hoffmann, L. Zhang, D. Go, Q. Li, A. Haghighirad, K. Sen, S. Blügel, M. Le Tacon, Y. Mokrousov, W. Wulfhekel, [Magnetic domain walls of the van der Waals material Fe3GeTe2](https://doi.org/10.1088/2053-1583/ac5d0e), _2D Materials_ **9,** 025022 (2022). +- P. Rüßmann, S. Blügel, [Density functional Bogoliubov-de Gennes analysis of superconducting Nb and Nb(110) surfaces](https://doi.org/10.1103/physrevb.105.125143), _Physical Review B_ **105,** no. 125143, (2022). +- M. Kotiuga, S. Halilov, B. Kozinsky, M. Fornari, N. Marzari, G. Pizzi, [Microscopic picture of paraelectric perovskites from structural prototypes](https://doi.org/10.1103/physrevresearch.4.l012042), _Physical Review Research_ **4,** no. L012042, (2022). +- M. Bonacci, M. Zanfrognini, E. Molinari, A. Ruini, M. Caldas, A. Ferretti, D. Varsano, [Excitonic effects in graphene-like C3n](https://doi.org/10.1103/physrevmaterials.6.034009), _Physical Review Materials_ **6,** no. 034009, (2022). +- H. Saßnick, C. Cocchi, [Exploring cesium–tellurium phase space via high-throughput calculations beyond semi-local density-functional theory](https://doi.org/10.1063/5.0082710), _The Journal of Chemical Physics_ **156,** (2022). +- Y. Wang, S. Kavanagh, I. Burgués-Ceballos, A. Walsh, D. Scanlon, G. Konstantatos, [Cation disorder engineering yields AgBiS2 nanocrystals with enhanced optical absorption for efficient ultrathin solar cells](https://doi.org/10.1038/s41566-021-00950-4), _Nature Photonics_ **16,** 235-241 (2022). +- B. Zhu, D. Scanlon, [Predicting Lithium Iron Oxysulfides for Battery Cathodes](https://doi.org/10.1021/acsaem.1c03094), _ACS Applied Energy Materials_ **5,** 575-584 (2022). + + +### Publications* from 2021 +_* This is an incomplete list of research papers that utilise AiiDA. Extracted manually from all citations of just these two articles ([Main](https://doi.org/10.1038/s41597-020-00638-4) and [Engine](https://doi.org/10.1016/j.commatsci.2020.110086))_ + +- S. Vijay, H. Kristoffersen, Y. Katayama, Y. Shao-Horn, I. Chorkendorff, B. Seger, K. Chan, [How to extract adsorption energies, adsorbate–adsorbate interaction parameters and saturation coverages from temperature programmed desorption experiments](https://doi.org/10.1039/d1cp01992a), _Physical Chemistry Chemical Physics_ **23,** 24396-24402 (2021). +- R. Goodall, B. Zhu, J. MacManus‐Driscoll, A. Lee, [Materials Informatics Reveals Unexplored Structure Space in Cuprate Superconductors](https://doi.org/10.1002/adfm.202104696), _Advanced Functional Materials_ **31,** (2021). +- C. Cocchi, H. Saßnick, [Ab Initio Quantum-Mechanical Predictions of Semiconducting Photocathode Materials](https://doi.org/10.3390/mi12091002), _Micromachines_ **12,** 1002 (2021). +- A. Jain, D. Marchand, A. Glensk, M. Ceriotti, W. Curtin, [Machine learning for metallurgy III: A neural network potential for Al-Mg-Si](https://doi.org/10.1103/physrevmaterials.5.053805), _Physical Review Materials_ **5,** no. 053805, (2021). +- T. Sohier, M. Gibertini, M. Verstraete, [Remote free-carrier screening to boost the mobility of Fröhlich-limited two-dimensional semiconductors](https://doi.org/10.1103/physrevmaterials.5.024004), _Physical Review Materials_ **5,** no. 024004, (2021). + + ### Publications from 2020 - M. Hope, B. Zhang, B. Zhu, D. M. Halat, J. L. MacManus-Driscoll, C. P. Grey, [Probing Interfaces in Complex Oxide Heterostructures via 17O Solid State NMR Spectroscopy](https://doi.org/10.26434/chemrxiv.12288332.v1), _ChemRxiv, Preprint_ (2020). - M. G. Mottet, [Accelerating materials discovery for solid state electrolytes](http://dx.doi.org/10.5075/epfl-thesis-7179), _EPFL THESIS_ (2020). - E. Bosoni, [Material Selection for Spin-Transfer-Torque Magnetic Random Access Memories: a High-Throughput approach](http://hdl.handle.net/2262/91467), PhD diss., Trinity College Dublin (2020). - J. S. Yu, J. H. Liao, Y. J. Zhao, Yin-Chang Zhao, and X. B. Yang, [Motif based high-throughput structure prediction of superconducting monolayer titanium boride](https://pubs.rsc.org/en/content/articlelanding/2020/CP/D0CP01540G#!divAbstract), _Physical Chemistry Chemical Physics_ **22,** no. 28, 16236-16243 (2020). -- A. Togo, Y. Inoue, and I. Tanaka, [Phonon structure of titanium under shear deformation along {10 1¯ 2} twinning mode](https://journals.aps.org/prb/abstract/10.1103/PhysRevB.102.024106), _Physical Review B_ **102**, no. 2, 024106 (2020). +- A. Togo, Y. Inoue, and I. Tanaka, [Phonon structure of titanium under shear deformation along {10 1¯ 2} twinning mode](https://doi.org/10.1103/PhysRevB.102.024106), _Physical Review B_ **102**, no. 2, 024106 (2020). - S. Mishra, X. Yao, Q. Chen, K. Eimre, O. Groening, R. Ortiz, M. Di Giovannantonio et al. [Giant magnetic exchange coupling in rhombus-shaped nanographenes with zigzag periphery](https://arxiv.org/abs/2003.03577). _arXiv preprint_ arXiv:2003.03577 (2020). - Q. Sun, X. Yao, O. Gröning, K. Eimre, C. A. Pignedoli, K. Müllen, A. Narita, R. Fasel, and P. Ruffieux, [Coupled spin states in armchair graphene nanoribbons with asymmetric zigzag edge extensions](https://pubs.acs.org/doi/10.1021/acs.nanolett.0c02077), _Nano letters_ **20**, no. 9, 6429-6436 (2020). - M. Kappeler, A. Marusczyk, and B. Ziebarth, [Simulation of nickel surfaces using ab-initio and empirical methods](https://www.sciencedirect.com/science/article/pii/S2589152920300922), _Materialia_ **12**, 100675 (2020). @@ -37,7 +111,7 @@ A list of publications containing calculations powered by AiiDA, selected from t - T. Sohier, M. Gibertini, and N. Marzari. [Profiling novel high-conductivity 2D semiconductors](https://iopscience.iop.org/article/10.1088/2053-1583/abc5d0/meta). _2D Materials_ **8**, no. 1, 015025 (2020). - A. García, N. Papior, A. Akhtar, E. Artacho, V. Blum, E. Bosoni, P. Brandimarte et al., [Siesta: Recent developments and applications](https://aip.scitation.org/doi/full/10.1063/5.0005077), _The Journal of chemical physics_ **152**, no. 20, 204108 (2020). - D. Ongari, L. Talirz, and B. Smit. [Too Many Materials and Too Many Applications: An Experimental Problem Waiting for a Computational Solution](https://pubs.acs.org/doi/abs/10.1021/acscentsci.0c00988). _ACS central science_ **6**, no. 11, 1890-1900 (2020). -- D. Marchand, A. Jain, A. Glensk, and W. A. Curtin, [Machine learning for metallurgy I. A neural-network potential for Al-Cu](https://journals.aps.org/prmaterials/abstract/10.1103/PhysRevMaterials.4.103601), _Physical Review Materials_ **4**, no. 10, 103601 (2020). +- D. Marchand, A. Jain, A. Glensk, and W. A. Curtin, [Machine learning for metallurgy I. A neural-network potential for Al-Cu](https://doi.org/10.1103/PhysRevMaterials.4.103601), _Physical Review Materials_ **4**, no. 10, 103601 (2020). - G. Pizzi, V. Vitale, R. Arita, S. Blügel, F. Freimuth, G. Géranton, M. Gibertini et al., [Wannier90 as a community code: new features and applications](https://iopscience.iop.org/article/10.1088/1361-648X/ab51ff/meta), *Journal of Physics: Condensed Matter* **32**, no. 16, 165902 (2020). - Y. Qu, X. Meng, Z. Jia, X. Liu, D. Liu, S. Li, and F. Bian. [Accelerating Materials Discovery Based on Generalized Low-dimensional Conformation Performance Relationships](https://iopscience.iop.org/article/10.1088/1757-899X/746/1/012020/meta). _IOP Conference Series: Materials Science and Engineering_, Vol. **746**. No. 1. (2020). - L. Kahle, A. Marcolongo, N. Marzari, [High-throughput computational screening for solid-state Li-ion conductors](http://doi.org/10.1039/c9ee02457c), _Energy & Environmental Science_ **13**, 928–948 (2020). @@ -84,4 +158,4 @@ A list of publications containing calculations powered by AiiDA, selected from t - G. Pizzi, M. Gibertini, E. Dib, N. Marzari, G. Iannaccone, G. Fiori, [Performance of arsenene and antimonene double-gate MOSFETs from first principles](http://doi.org/10.1038/ncomms12585), _Nature Communications_ **7** (2016). - M. Gibertini, G. Pizzi, N. Marzari, [Engineering polar discontinuities in honeycomb lattices](http://doi.org/10.1038/ncomms6157), _Nature Communications_ **5** (2014). -Last updated: **March 2021** +Last updated: **March 2024** diff --git a/docs/sections/team.md b/docs/sections/team.md index 8225a48..9382a7e 100644 --- a/docs/sections/team.md +++ b/docs/sections/team.md @@ -16,22 +16,18 @@ Besides the AiiDA team at EPFL listed below, we thank our [numerous external cod * - ![Portrait](../pics/team/simon.jpg) - **Simon Adorf**\ *PostDoc Research Scientist, Theory and Simulation of Materials, EPFL*\ - [epfl.ch](https://people.epfl.ch/simon.adorf) * - ![Portrait](../pics/team/marnik.jpg) - **Marnik Bercx**\ *PostDoc Research Scientist, Theory and Simulation of Materials, EPFL*\ - [epfl.ch](https://people.epfl.ch/marnik.bercx) * - ![Portrait](../pics/team/dossantos.jpg) - **Flaviano Dos Santos**\ *PostDoc Research Scientist, Theory and Simulation of Materials, EPFL*\ - [epfl.ch](https://people.epfl.ch/flaviano.dossantos) * - ![Portrait](../pics/team/huber.png) - **Sebastiaan P. Huber**\ *PostDoc Research Scientist, Theory and Simulation of Materials, EPFL*\ - [epfl.ch](https://people.epfl.ch/sebastiaan.huber) * - ![Portrait](../pics/team/boris.png) - **Boris Kozinsky**\ @@ -51,22 +47,18 @@ Director, National Centre for Competence in Research NCCR MARVEL, EPFL*\ * - ![Portrait](../pics/team/Ramirez.jpg) - **Francisco F. Ramirez**\ *PostDoc Research Scientist, Theory and Simulation of Materials, EPFL*\ - [epfl.ch](https://people.epfl.ch/francisco.ramirez) * - ![Portrait](../pics/team/talirz.jpg) - **Leopold Talirz**\ *PostDoc Research Scientist, Theory and Simulation of Materials, EPFL*\ - [epfl.ch](https://people.epfl.ch/leopold.talirz) * - ![Portrait](../pics/team/Yakutovich.jpg) - **Aliaksandr Yakutovich**\ *PostDoc Research Scientist, Theory and Simulation of Materials, EPFL*\ - [epfl.ch](https://people.epfl.ch/aliaksandr.yakutovich) * - ![Portrait](../pics/team/JusongYu.jpg) - **Jusong Yu**\ *PostDoc Research Scientist, Theory and Simulation of Materials, EPFL*\ - [epfl.ch](https://people.epfl.ch/jusong.yu) ::: diff --git a/docs/sections/testimonials.md b/docs/sections/testimonials.md index a969504..dcd600c 100644 --- a/docs/sections/testimonials.md +++ b/docs/sections/testimonials.md @@ -35,6 +35,9 @@ researcher at National Institute for Materials Science (NIMS), Japan** Literature references --------------------- +**Malcolm Sim; The Dynamic Orchestration of Self-Driving Laboratories. Master's thesis, University of Toronto, 2024.** [Availabe from](https://tspace.library.utoronto.ca/bitstream/1807/138140/2/Sim_Malcolm_202403_MSc_thesis.pdf) +> \[…\] To tackle the computational challenges and ensure reproducibility, ChemOS 2.0 embraces the integration of the AiiDA software package. AiiDA plays a critical role in automating data transfers between the user’s local environment and the high-performance supercomputing cluster. […\] Additionally, AiiDA is prepared for distributed computing, enabling efficient utilization of computational resources. + **Foscato, M.; Jensen, V. R. Automated in Silico Design of Homogeneous Catalysts. ACS Catal. 2020, 10 (3), 2354–2377.** [10.1021/acscatal.9b04952](https://doi.org/10.1021/acscatal.9b04952) > \[…\] Such reuse and repurposing may be realized by making sure that workflow managers such as AiiDA, QMflows, AFlow, Signac, and FireWorks prepare job summaries in standardized data formats used by the community repositories. The most detailed management control is currently offered by AiiDA which keeps track of the complete history, including information on methods, input parameters, computer, postprocessing tools, and dependencies, leading to a computational result, thereby mapping the complete data provenance necessary to ensure reproducibility and repurposing. \[…\] diff --git a/requirements.txt b/requirements.txt index bc5ae1b..e82e3d2 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,7 +1,9 @@ -myst-parser~=0.18.0 -pydata-sphinx-theme==0.12.0rc1 +sphinx~=8.0.0 +myst-parser~=4.0.0 +pydata-sphinx-theme~=0.15.4 ablog~=0.10.25 -sphinx-design~=0.3.0 +sphinx-design~=0.6.1 sphinx_subfigure~=0.2.4 -sphinx-notfound-page~=0.8.3 +sphinx-notfound-page~=1.0.4 sphinx-timeline~=0.2.1 +sphinx_favicon~=1.0.1 diff --git a/tox.ini b/tox.ini index 8b5baeb..697d686 100644 --- a/tox.ini +++ b/tox.ini @@ -23,4 +23,4 @@ deps = -rrequirements.txt allowlist_externals = rm commands_pre = rm -rf docs/_build/htlinkcheckml -commands = sphinx-build -b linkcheck docs/ docs/_build/linkcheck +commands = sphinx-build -b linkcheck docs/ docs/_build/linkcheck --color