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make AiiDAlab cluster the first tab
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mbercx committed May 27, 2021
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46 changes: 23 additions & 23 deletions docs/index.rst
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Expand Up @@ -36,6 +36,29 @@ You could also use the AiiDAlab demo cluster, but since it can only handle a lim

.. tabs::

.. tab:: AiiDAlab cluster

+-----------------+-----------------------------------------------------------------------------------------------------------+
| Related resources |
+=================+===========================================================================================================+
| AiiDAlab | `AiiDAlab docker stack 21.02.1`_, `AiiDAlab k8s deployment`_ |
+-----------------+-----------------------------------------------------------------------------------------------------------+
| python packages | `aiida-core 1.5.2`_, `aiida-quantumespresso 3.3.0`_ |
+-----------------+-----------------------------------------------------------------------------------------------------------+
| codes | `Quantum ESPRESSO 6.0.0`_ |
+-----------------+-----------------------------------------------------------------------------------------------------------+

The |AiiDAlab demo cluster| is a Jupyter-based web platform installed on a cluster that can run some basic calculations for demonstration and tutorial purposes.
Simply click the link and log in with the EGI check-in.

The first part of the tutorial will be run in the terminal.
Just click on the "Terminal" icon in the header to open one in a new tab.

.. figure:: source/images/AiiDAlab_header-terminal.png
:width: 100%

Once the terminal is opened, you're all set to get started with the tutorial!

.. tab:: Quantum Mobile

+-----------------+-----------------------------------------------------------------------------------------------------------+
Expand Down Expand Up @@ -76,29 +99,6 @@ You could also use the AiiDAlab demo cluster, but since it can only handle a lim
If you see all green check marks, you're ready to start with the tutorial!

.. tab:: AiiDAlab cluster

+-----------------+-----------------------------------------------------------------------------------------------------------+
| Related resources |
+=================+===========================================================================================================+
| AiiDAlab | `AiiDAlab docker stack 21.02.1`_, `AiiDAlab k8s deployment`_ |
+-----------------+-----------------------------------------------------------------------------------------------------------+
| python packages | `aiida-core 1.5.2`_, `aiida-quantumespresso 3.3.0`_ |
+-----------------+-----------------------------------------------------------------------------------------------------------+
| codes | `Quantum ESPRESSO 6.0.0`_ |
+-----------------+-----------------------------------------------------------------------------------------------------------+

The |AiiDAlab demo cluster| is a Jupyter-based web platform installed on a cluster that can run some basic calculations for demonstration and tutorial purposes.
Simply click the link and log in with the EGI check-in.

The first part of the tutorial will be run in the terminal.
Just click on the "Terminal" icon in the header to open one in a new tab.

.. figure:: source/images/AiiDAlab_header-terminal.png
:width: 100%

Once the terminal is opened, you're all set to get started with the tutorial!

Hands-on materials
------------------

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85 changes: 42 additions & 43 deletions docs/source/sections/qe.rst
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Expand Up @@ -92,30 +92,6 @@ This will depend on whether you are running the tutorial in the Quantum Mobile o

.. tabs::

.. tab:: Quantum Mobile

Let's have a look at the codes in our database with the ``verdi shell``:

.. code-block:: console
$ verdi code list
# List of configured codes:
# (use 'verdi code show CODEID' to see the details)
* pk 1 - qe-3.4.0-pw@localhost
* pk 2 - qe-3.4.0-cp@localhost
* pk 3 - qe-3.4.0-pp@localhost
* pk 4 - qe-3.4.0-ph@localhost
* pk 5 - qe-3.4.0-neb@localhost
* pk 6 - qe-3.4.0-projwfc@localhost
* pk 7 - qe-3.4.0-pw2wannier90@localhost
* pk 8 - qe-3.4.0-q2r@localhost
* pk 9 - qe-3.4.0-dos@localhost
* pk 10 - qe-3.4.0-matdyn@localhost
As you can see, this Quantum Mobile virtual machine already comes with all of the Quantum ESPRESSO codes set up in the AiiDA database.
The code we will be running is the ``pw.x`` code, set up under the label ``qe-3.4.0-pw`` on the ``localhost`` computer.
Make a note of the PK or label of the code, since you'll need to replace it in code snippets later in this tutorial.

.. tab:: AiiDAlab cluster

Let's have a look at the codes in our database with the ``verdi shell``:
Expand Down Expand Up @@ -146,6 +122,30 @@ This will depend on whether you are running the tutorial in the Quantum Mobile o
Make a note of the PK or label of the code, since you'll need to replace it in code snippets later in this tutorial.

.. tab:: Quantum Mobile

Let's have a look at the codes in our database with the ``verdi shell``:

.. code-block:: console
$ verdi code list
# List of configured codes:
# (use 'verdi code show CODEID' to see the details)
* pk 1 - qe-3.4.0-pw@localhost
* pk 2 - qe-3.4.0-cp@localhost
* pk 3 - qe-3.4.0-pp@localhost
* pk 4 - qe-3.4.0-ph@localhost
* pk 5 - qe-3.4.0-neb@localhost
* pk 6 - qe-3.4.0-projwfc@localhost
* pk 7 - qe-3.4.0-pw2wannier90@localhost
* pk 8 - qe-3.4.0-q2r@localhost
* pk 9 - qe-3.4.0-dos@localhost
* pk 10 - qe-3.4.0-matdyn@localhost
As you can see, this Quantum Mobile virtual machine already comes with all of the Quantum ESPRESSO codes set up in the AiiDA database.
The code we will be running is the ``pw.x`` code, set up under the label ``qe-3.4.0-pw`` on the ``localhost`` computer.
Make a note of the PK or label of the code, since you'll need to replace it in code snippets later in this tutorial.

To run the SCF calculation, we'll also need to provide the family of pseudopotentials.
These can be installed easily using the ``aiida-pseudo`` package:

Expand Down Expand Up @@ -421,14 +421,6 @@ How you can open this file will depend on the platform you are running the tutor

.. tabs::

.. tab:: Quantum Mobile

You can simply use the ``evince`` command to open the ``.pdf`` that contains the provenance graph:

.. code-block::
$ evince <PK>.dot.pdf
.. tab:: AiiDAlab cluster

If you open a *file manager* on the starting page of the AiiDA JupyterHub:
Expand All @@ -438,6 +430,14 @@ How you can open this file will depend on the platform you are running the tutor

You should be able to use the file manager to navigate to and open the PDF.

.. tab:: Quantum Mobile

You can simply use the ``evince`` command to open the ``.pdf`` that contains the provenance graph:

.. code-block::
$ evince <PK>.dot.pdf
Let's have a look at one of the outputs, i.e. the ``output_parameters``.
You can get the contents of this dictionary easily using the ``verdi shell``:

Expand Down Expand Up @@ -561,16 +561,6 @@ How you can access the REST API web-interface will depend on where you are execu

.. tabs::

.. tab:: Quantum Mobile

Open the |provenance browser| **in a browser inside the virtual machine** and copy the following URL into the text box:

.. code-block::
http://127.0.0.1:5000/api/v4
Then simply click "Go!" to start exploring your data!

.. tab:: AiiDAlab cluster

Since this AiiDAlab instance is running on a remote machine, we need to expose the REST API to a public URL.
Expand All @@ -596,6 +586,16 @@ How you can access the REST API web-interface will depend on where you are execu
then the URL you should provide the provenance browser is ``https://bb84d27809e0.eu.ngrok.io/api/v4`` (see the last ``Forwarding`` line).
Then simply click "Go!" to start exploring your data!

.. tab:: Quantum Mobile

Open the |provenance browser| **in a browser inside the virtual machine** and copy the following URL into the text box:

.. code-block::
http://127.0.0.1:5000/api/v4
Then simply click "Go!" to start exploring your data!

.. |provenance browser| raw:: html

<a href="https://www.materialscloud.org/explore/connect" target="_blank">Materials Cloud Explore section</a>
Expand Down Expand Up @@ -634,7 +634,6 @@ This will take us to the `details` view of that particular node:

The `details` view of a specific node of type ``BandsData``.


We can see that the Explore Section can visualize the band structure stored in a ``BandsData`` node.
It also shows (as it does for all types of nodes) the `AiiDA Provenance Browser` on its right.
This tool allows us to easily explore the connections between nodes and understand, for example, how these results were obtained.
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