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Small improvements and typo corrections. (#311)
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Updated text and versions.

Co-authored-by: Flaviano José dos Santos <flavianojs@Flavianos-MacBook-Pro.local>
Co-authored-by: Marnik Bercx <mbercx@gmail.com>
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26 changes: 11 additions & 15 deletions docs/index.rst
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Expand Up @@ -3,22 +3,18 @@ AiiDA ABC tutorial

.. _ABC_2021_Homepage:

.. todo::

Update versions to ones from Quantum Mobile image

+-----------------+-----------------------------------------------------------------------------------------------------------+
| Related resources |
+=================+===========================================================================================================+
| python packages | `aiida-core XXXX`_, `aiida-quantumespresso XXXX`_ |
| python packages | `aiida-core 1.3.0`_, `aiida-quantumespresso 3.0.0`_ |
+-----------------+-----------------------------------------------------------------------------------------------------------+
| codes | `Quantum ESPRESSO XXXX`_ |
| codes | `Quantum ESPRESSO 6.5`_ |
+-----------------+-----------------------------------------------------------------------------------------------------------+

.. _Quantum Mobile 20.03.1: https://github.com/marvel-nccr/quantum-mobile/releases/tag/20.03.1
.. _aiida-core XXXX: https://pypi.org/project/aiida-core/1.4.3/
.. _aiida-quantumespresso XXXX: https://github.com/aiidateam/aiida-quantumespresso/releases/tag/v3.2.1
.. _Quantum ESPRESSO XXXX: https://github.com/QEF/q-e/releases/tag/qe-6.0.0
.. _aiida-core 1.3.0: https://pypi.org/project/aiida-core/1.3.0/
.. _aiida-quantumespresso 3.0.0: https://github.com/aiidateam/aiida-quantumespresso/releases/tag/v3.0.0
.. _Quantum ESPRESSO 6.5: https://github.com/QEF/q-e/releases/tag/qe-6.5

This is the content of the virtual AiiDA tutorial organised for the University of ABC on the 10th of February 2021.

Expand All @@ -30,7 +26,7 @@ The tutorial will be run on the |AiiDAlab tutorials cluster|, just click the lin
.. important::

Note down your password so that you can login again in case you get inadvertently logged out.
In case your forgot your password, either just create a new account (and lose previous progress) or contact one of the administrators to reset your password.
In case you forgot your password, either just create a new account (and lose previous progress) or contact one of the administrators to reset your password.

It will take a few minutes for your server to start up on first login, after that you are all set and ready to start with the tutorial!

Expand Down Expand Up @@ -63,12 +59,12 @@ If you want to learn more, you can check the `2020 AiiDA virtual tutorial <https
Acknowledgements
----------------

.. todo::

Update Acknowledgements

This event was made possible by support from XXXX.
This event was made possible by support from the MaX European Centre of Excellence, the MARVEL National Centre of Competence in Research and the H2020 INTERSECT project.

.. image:: source/sponsors/max.png
:target: http://www.max-centre.eu/
:width: 35%

.. image:: source/sponsors/INTERSECT_logo.png
:target: https://intersect-project.eu/
:width: 7%
10 changes: 7 additions & 3 deletions docs/source/sections/data.rst
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Expand Up @@ -4,7 +4,11 @@
Working with data and querying your results
*******************************************

In this section of the tutorial we will focus on how to organise and explore the data in an AiiDA database, based on a previously created database for this tutorial.
.. todo::

Probably requires update.

In this section of the tutorial, we will focus on how to organise and explore the data in an AiiDA database, based on a previously created database for this tutorial.
To follow the tutorial, you first need to import that archive into your database:

.. code-block:: console
Expand All @@ -17,7 +21,7 @@ How to group nodes

AiiDA's database is great for automatically storing all your data, but sometimes it can be tricky to navigate this flat data store.
To create some order in this mass of data, you can *group* sets of nodes together, just as you would with files in folders on your filesystem.
Each group instance can hold any amount of nodes and any node can be contained in any number of groups.
Each group can hold any amount of nodes and any node can be contained in any number of groups.
A typical use case is to store all nodes that share a common property in a single group.

Listing existing groups
Expand Down Expand Up @@ -151,7 +155,7 @@ and finally to remove the group entirely:
Organising groups in hierarchies
--------------------------------

Earlier we mentioned that groups are like files in folders on your filesystem.
Earlier, we mentioned that groups are like files in folders on your filesystem.
As with folders and sub-folders then, as the amount of groups we have grows, we may also wish to structure our groups in a hierarchy.
Groups in AiiDA are inherently "flat", in that groups may only contain nodes and not other groups.
However it is possible to construct *virtual* group hierarchies based on delimited group labels, using the ``grouppath`` utility.
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11 changes: 6 additions & 5 deletions docs/source/sections/qe.rst
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Expand Up @@ -7,7 +7,7 @@ Let's start with a quick demo of how AiiDA can make your life easier as a comput

.. note::

Throughout this tutorial we will be using the ``verdi`` command line interface.
Throughout this tutorial we will be using the ``verdi`` command line interface (CLI).
Here's couple of tricks that will make your life easier:

* The ``verdi`` command supports **tab-completion**:
Expand Down Expand Up @@ -84,8 +84,8 @@ The PK and UUID both reference the node with the only difference that the PK is
Running a calculation
---------------------

We'll start with running a simple SCF calculation with `Quantum ESPRESSO`_ for the structure we just imported.
First we'll have to set up the code in our database.
We'll start with running a simple self-consistent field calculation (SCF) with `Quantum ESPRESSO`_ for the structure we just imported.
First, we'll have to set up the `Quantum ESPRESSO` code in our database.
This can be done with the following ``verdi`` CLI command:

.. code-block:: console
Expand Down Expand Up @@ -119,7 +119,7 @@ To see if the pseudopotential families have been installed correctly, do:
Success: * SSSP_1.1_efficiency [85 pseudos]
Success: * SSSP_1.1_precision [85 pseudos]
Along with the PK of the ``StructureData`` node for the silicon structure we imported in the previous section, we now have everything to set up the calculation step by step.
Along with the PK of the ``StructureData`` node for the silicon structure that we imported in the previous section, we now have everything to set up the calculation step by step.
We will do this in the ``verdi shell``, an interactive IPython shell that has many basic AiiDA classes pre-loaded.
To start the IPython shell, simply type in the terminal:

Expand Down Expand Up @@ -433,7 +433,8 @@ In most cases, the full provenance graph obtained from ``verdi node graph genera
To see this for yourself, you can try to generate the one for the work chains ran by the `Quantum ESPRESSO`_ app, or for the workchain script of the last section.
It therefore becomes very useful to learn how to browse the provenance interactively instead.

To do so, we need first to start the AiiDA REST API:
To do so, we will use the AiiDA REST API, which is a web-based interface for us to communicate with AiiDA.
Let's start the AiiDA REST API:

.. code-block:: console
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