use Phenylacetylene as XPS example

docs/source/howto/xps.rst

@@ -4,7 +4,7 @@ How to calculate XPS spectra
 
 Overview
 ========
-This tutorial will guide you through the process of setting up and running an XPS calculation for CH\ :sub:`3`\CHO molecule.
+This tutorial will guide you through the process of setting up and running an XPS calculation for Phenylacetylene molecule.
 
 
 Steps
@@ -15,7 +15,7 @@ To start, go ahead and :doc:`launch </installation/launch>` the app, then follow
 
 Step 1 Select a structure
 --------------------------------
-For this tutorial task, please use the `From Example` tab, and select the CH\ :sub:`3`\CHO molecule structure.
+For this tutorial task, please use the `From Example` tab, and select the Phenylacetylene molecule structure.
 
 In the end, click the `Confirm` button.
 
@@ -31,7 +31,6 @@ In the **Basic Setting** tab, set the parameters which are highlighted as follow
 - In the **Structure optimization** section, select ``Structure as is``.
 - Set **Electronic Type** to ``Insulator``
 - In the **properties** section, select ``X-ray photoelectron spectroscopy (XPS)``
-- In the **protocol** section, please select `fast` as the protocol for this calculation, in order to quickly get the result.
 
 
 Then go to the **Advanced settings** tab, navigate to `Accuracy and precision`, tick the `Override` box on the right-hand-side and in the dropdown box under `Exchange-correlation functional` select `PBE`.
@@ -56,23 +55,23 @@ Then, lick the **Confirm** button.
 
 Step 3 Choose computational resources
 ---------------------------------------
+We need to use a `pw` code on the high-performance computer to run XPS calculation for this system.
+Please read the relevant :doc:`How-To </howto/setup_computer_code>` section to setup code on a remote machine.
 
-For this small system, we can use the local computer (``localhost``) to run the calculation. The code ``pw-7.2@localhost`` should already be selected by default.
+In the **Resources** section, you can set the number of CPUs to 16.
 
-In the **Resources** section, you can set the number of CPUs to 4 for the test.
-
-Then, click the **Submit** button.
-
-.. note::
+.. image:: ../_static/images/xps_step_3.png
+   :align: center
 
-   In pratice, one usually need high-performance computer to run XPS calculation for large system. Please read the relevant :doc:`How-To </howto/setup_computer_code>` section to setup code on a remote machine.
 
+Then, click the **Submit** button.
 
 
 
 Step 4 Check the status and results
 -----------------------------------------
-The job may take ~2 minutes to finish.
+The job may take 5~10 minutes to finish if your jobs are running immediately without waiting in the queue.
+
 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 `XPS` tab.
 
@@ -85,19 +84,28 @@ Here is the result of the XPS calculation.
 You can click the **Binding energy** button to view the calculated binding energies.
 You can change which element to view XPS spectra for using the dropdown box in the top left.
 
-.. figure:: /_static/images/xps_step_4.png
+.. figure:: /_static/images/xps_step_4_xps_tab.png
    :align: center
 
+One can upload the experimental XPS spectra, and compare to the calculated XPS spectra.
+There is a button on the bottom left of the XPS tab to upload the experimental data.
+Here is an example of the comparison between the calculated and experimental XPS spectra [1] for the C_1s core level of Phenylacetylene.
+
+.. figure:: /_static/images/xps_step_4_pa_exp.png
+   :align: center
+
+The calculated spectra agrees well with the experimental data, underscoring the reliability of DFT calculations.
+
+
 .. tip::
 
-   One can read the exact binding energies from the the output of the calculation, by clicking the `outputs` tab on the node tree of the WorkChain, as shown below.
+   One can also read the exact binding energies from the the output of the calculation, by clicking the `outputs` tab on the node tree of the WorkChain, as shown below.
 
    .. figure:: /_static/images/xps_step_4_output.png
       :align: center
 
 
-   When comparing the these binding energies to the experimental data, please correct the energies by the given offset listed in the ``Offset Energies`` table in the button of the XPS result tab.
-   Besides, the DFT calculated binding energies do not include spin-orbit splitting of the core level state.
+   The DFT calculated binding energies do not include spin-orbit splitting of the core level state.
    We can include the spin-orbit splitting using its experimental value.
    Take `f` orbit as a example, we need subtracting :math:`3/7` of the experimental spin-orbit splitting or adding :math:`4/7` of the DFT calculated value, to get the position of the :math:`4f_{7/2}` and :math:`4f_{5/2}` peaks, respectively. Here is a table of the spin-orbit splitting for different orbitals.
 
@@ -113,40 +121,45 @@ You can change which element to view XPS spectra for using the dropdown box in t
    | 4f             | :math:`3/7`       |  :math:`4/7`      |
    +----------------+-------------------+-------------------+
 
+
+
 Congratulations, you have finished this tutorial!
 
 
-A real world example
+Another example
 ====================
-ETFA is commonly used as example for XPS measurements and calculations due to the extreme chemical shifts of its four different carbon atoms. [1]
+ETFA is commonly used as example for XPS measurements and calculations due to the extreme chemical shifts of its four different carbon atoms. [2]
 
 .. tip::
 
    One can select the ETFA molecule from the `From Example` tab, and follow the same steps as above to run the XPS calculation for this molecule.
-   One need use a high-performance computer to run XPS calculation for this system. Please read the relevant :doc:`How-To </howto/setup_computer_code>` section to setup code on a remote machine.
-
 
 Here is the result of the XPS calculation for the ETFA molecule.
 
-
 .. figure:: /_static/images/xps_etfa_dft.png
    :align: center
 
-Here is the chemical shift from experiment. [1]
+Here is the chemical shift from experiment. [2]
 
 .. figure:: /_static/images/xps_etfa_exp.jpg
    :align: center
 
 
 The calculated relative shifts align well with the trends observed in experimental data, underscoring the reliability of DFT calculations.
-Although there are minor discrepancies in the absolute shift values, this is a recognized limitation stemming from the approximations in the exchange-correlation functional within DFT frameworks. [2]
+Although there are minor discrepancies in the absolute shift values, this is a recognized limitation stemming from the approximations in the exchange-correlation functional within DFT frameworks. [3]
 
 Questions
 =========
 
 If you have any questions, please, do not hesitate to ask on the AiiDA discourse forum: https://aiida.discourse.group/.
 
-[1] O. Travnikova *et al.*, , *Relat. Phenom.* 185, 191 (2012)
-https://doi.org/10.1016/j.elspec.2012.05.009
-[2] B.P. Klein  *et al.*, , *J. Phys. Condens. Matter* 33, 154005 (2021)
-https://doi.org/10.1088/1361-648X/abdf00
+
+
+References
+==========
+
+[1] G.Iucci, *et al.*, *Chem. Phys.* 300, 13 (2004) https://doi.org/10.1016/j.chemphys.2004.03.012
+
+[2] O. Travnikova, *et al.*, , *Relat. Phenom.* 185, 191 (2012) https://doi.org/10.1016/j.elspec.2012.05.009
+
+[3] B.P. Klein,  *et al.*, , *J. Phys. Condens. Matter* 33, 154005 (2021) https://doi.org/10.1088/1361-648X/abdf00

src/aiidalab_qe/app/structure/__init__.py

@@ -33,7 +33,7 @@
     ("Gold (fcc)", file_path / "examples" / "Au.cif"),
     ("Cobalt (hcp)", file_path / "examples" / "Co.cif"),
     ("Lithium carbonate", file_path / "examples" / "Li2CO3.cif"),
-    ("CH3CHO molecule", file_path / "examples" / "CH3CHO.xyz"),
+    ("Phenylacetylene molecule", file_path / "examples" / "Phenylacetylene.xyz"),
     ("ETFA molecule", file_path / "examples" / "ETFA.xyz"),
 ]
 

src/aiidalab_qe/app/structure/examples/Phenylacetylene.xyz

@@ -0,0 +1,16 @@
+14
+Lattice="17.572400000000002 0.0 0.0 0.0 14.3161 0.0 0.0 0.0 10.0002" Properties=species:S:1:pos:R:3 pbc="T T T"
+C        8.87580000       7.15810000       5.00010000
+C        8.17830000       8.36610000       5.00010000
+C        8.17830000       5.95000000       5.00010000
+C        6.78350000       8.36630000       5.00010000
+C        6.78340000       5.95020000       5.00010000
+C        6.08610000       7.15830000       5.00010000
+C       10.30480000       7.15810000       5.00010000
+C       11.50750000       7.15840000       5.00010000
+H        8.70750000       9.31610000       5.00000000
+H        8.70750000       5.00000000       5.00010000
+H        6.24030000       9.30680000       5.00010000
+H        6.24010000       5.00980000       5.00010000
+H        5.00000000       7.15830000       5.00020000
+H       12.57240000       7.15850000       5.00020000