add doc

docs/source/index.rst

@@ -10,6 +10,7 @@ AiiDA plugin for `Bader <https://theory.cm.utexas.edu/henkelman/code/bader/>`_ c
 
    quick_start
    installation
+   qeapp.rst
 
 
 

docs/source/qeapp.rst

@@ -0,0 +1,94 @@
+======================================
+How to calculate Bader charge in QEApp
+======================================
+
+Overview
+========
+This tutorial will guide you through the process of setting up and running Bader charge in QEApp calculation for LiCoO\ :sub:`2`.
+
+
+Steps
+=====
+
+To start, go ahead and :doc:`launch </installation/launch>` the app, then follow the steps below.
+
+
+Step 1 Select a structure
+--------------------------------
+For this tutorial task, please use the `From Examples` tab, and select the LiCoO\ :sub:`2` structure.
+
+Click the `Confirm` button to proceed.
+
+.. figure:: /_static/images/bader_step_1.png
+   :align: center
+
+
+Step 2 Configure workflow
+--------------------------------
+
+In the **Basic Settings** tab, set the following parameters:
+
+- In the **Structure optimization** section, select ``Structure as is``.
+- Set **Electronic Type** to ``Insulator``
+- In the **properties** section, select ``Bader charge analysis``
+
+.. image:: ../_static/images/bader_step_2_basic_setting.png
+   :align: center
+
+
+Click the **Confirm** button to proceed.
+
+
+Step 3 Choose computational resources
+---------------------------------------
+In this small system, we can use the default `localhost` computer to run the calculation.
+
+
+.. tip::
+   For large system, we need the high-performance computer to run Bader charge calculation.
+   Please read the relevant :doc:`How-To </howto/setup_computer_code>` section to setup code on a remote machine.
+
+Set the number of CPUs/nodde to 4.
+
+
+.. image:: ../_static/images/bader_step_3.png
+   :align: center
+
+
+Then, click the **Submit** button.
+
+
+
+Step 4 Check the status and results
+-----------------------------------------
+The job may take 2~4 minutes to finish.
+
+While the calculation is running, you can monitor its status as shown in the :ref:`basic tutorial <basic_status>`.
+When the job is finished, you can view result spectra in the `Bader Charge` tab.
+
+.. tip::
+
+   If the `Bader Charge` tab is now shown when the jobs is finished.
+   Click the ``QeAppWorkChain<pk>`` item on top of the nodetree to refresh the step.
+
+Here is the result of the calculation. It includes:
+- the Bader charge data for the structure
+- the Structure viewer
+
+Click on the row above to highlight the specific atom whose Bader charge is being calculated.
+
+
+.. figure:: /_static/images/bader_step_4_xps_tab.png
+   :align: center
+
+
+
+
+Congratulations, you have finished this tutorial!
+
+
+
+Questions
+=========
+
+If you have any questions, please, do not hesitate to ask on the AiiDA discourse forum: https://aiida.discourse.group/.