'''<big>This is the optional experiment which may be chosen by any third year student. If you are looking for the Programming-Ising experiment, you will find it [[Third_year_CMP_compulsory_experiment|here]].</big>'''

<blockquote>
= Understanding trends in catalytic activity for hydrogen evolution =

</blockquote>This is the welcome page for the computational experiment about trends in catalytic activity for hydrogen evolution, part of the third year computational chemistry lab.

This computational experiment has been developed by Dr. Clotilde Cucinotta.

The computational experiment will be from 10:00 to 17:00 on Monday, Tuesday, Thursday and Friday. During these 4 days demonstrators will be available to answer all your questions.

'''There is an introductory lecture to the lab at 10:00 on the Start Date of your session. See the section 'Structure of the Experiment' below.'''

'''The deadline is at 12:00 noon on Wed of the week following the experiment.'''

Work submitted late will be penalised according to the [https://www.imperial.ac.uk/media/imperial-college/administration-and-support-services/registry/academic-governance/public/academic-policy/marking-and-moderation/Late-submission-Policy.pdf Late Submission Policy].

There is a link set up on [http://bb.imperial.ac.uk Blackboard] for submitting the report in PDF format and a .zip folder with all the input files and the output files produced during the experiment, in 3rd Year Chemistry Laboratories (2020 - 2021) / Y3C Third Year Computational Laboratory/;

Please note that the submission boxes will appear only once you have completed the curriculum review.

'''Your report will be marked out of 20'''.

The provided [https://imperialcollegelondon.box.com/s/rfck2ruyh7xyrg7pbth1cxqwqqj7rnta template] for the report contains a number questions and sub-questions. The final report is expected to contain answers to all these questions.

Questions related to this computational experiment can be directed to the demonstrators, Dr Yueyu Zhang and Ms. Margherita Buraschi via
[https://teams.microsoft.com/l/channel/19%3ad0b2cfbabd994931bf16dd1435472e58%40thread.tacv2/comp_lab__catalytic_activity?groupId=577dc55a-ed12-45f5-b092-dfa9e184e14b&tenantId=2b897507-ee8c-4575-830b-4f8267c3d307 Teams]

Their availability is specified below:
{| class="wikitable"
|+
|-
! !! Monday !! Tuesday !! Thursday !! Friday
|-
| Margherita || 15:30-16:30 || 10:00-11:00 || 14:00-15:00 || 14:00-15:00
|-
| Yueyu || 11:00-12:00 || 14:00-15:00 || 10:00-11:00 || 10:00-11:00
|}

Outside the time in which the demonstrators are available, all your questions should be posted in the forum on Blackboard.

== Introduction ==

In the electrochemistry course you learned about an important quantity, the exchange current, and how it reflects how viable is the reaction kinetics of an electrochemical transformation.

In this experiment you will predict what is the most efficient metal catalyst for hydrogen evolution by plotting the adsorption energy for hydrogen on different metals versus the measured exchange currents for this reaction. According to the Sabatier principle (named after the chemist Paul Sabatier), high catalytic activity is associated to an interaction between reactants and catalysts, which needs to be neither too strong nor too weak. As a consequence, the plot will have a maximum corresponding to the to the most active catalyst and the ideal adsorption energy: you will observe a so-named volcano plot.

You will learn how to:
*Evaluate the chemisorption energy for an atomic species on a metal;
*generate a ''volcano plot'' describing trends in catalytic activity for Hydrogen evolution;
*use the most basic feature of Unix operating system and work remotely on our hpc cluster login.hpc.ic.ac.uk;
*use a quantum-mechanical programme, [http://www.cp2k.org CP2K], which implements Density Functional Theory (DFT), to calculate the adsorption energies for Hydrogen on the closely packed surfaces of different metals;
*control and evaluate
**the numerical error in your DFT calculations
**the error associated to the selection of simulation parameters such as set of k points used to sample the Brillouin zone and the basis set used to expand the orbitals. Predict the equilibrium lattice parameters for a metal;
*extract from these calculations optimised geometries and energies, and evaluate adsorption energies;
*use a visualization programme to represent relaxation trajectories and optimised configurations.

'''<big>Please go through the following [https://imperialcollegelondon.box.com/s/ywmzgzfibmj13v7v1c9lpbr3n72d148x introductory technical notes] and [https://imperialcollegelondon.box.com/s/f0ai7bmg32x5mlm5gmvxiyu4sodzs2hd theoretical notes] references therein.</big>'''

Please note that:
 '''To run this experiment, you will need access to the Imperial College supercomputers. If you have VPN installed, you should be able to access the computers directly, via browser'''

*'''In order to connect to the hpc cluster via browser you need to activate [https://www.imperial.ac.uk/admin-services/ict/self-service/connect-communicate/remote-access/virtual-private-network-vpn/ using VPN]'''

*'''If you have not yet installed VPN, you may use [https://www.imperial.ac.uk/admin-services/ict/self-service/connect-communicate/remote-access/remotely-access-my-college-computer/remote-desktop-access-for-students/ Remote Desktop connection] (VPN not needed)

* to plot the graphs produced during this computational experiment you might want to use [https://www.anaconda.com/products/individual Anaconda] and use Jupiter notebook. Please install them if you will use these tools to make a picture of the Volcano plot.

== Instructions ==

To connect to our cluster your will need to digit the address line below in your browser:

login.hpc.ic.ac.uk

In this way you will launch an interactive session which will open a remote terminal on our cluster:

[[File:Termina.png|400px|thumb|centre|Remote terminal]]

Once you insert your credentials (your Imperial's user name and password) you are on our hpc cluster and can launch your calculations. Since there is no graphical interface available for CP2K code, you will need to submit your calculations from command line using the Unix operating system of our cluster, so the first step is to learn the basics of Unix.

=== Unix induction tutorial ===

To carry out the Unix induction tutorial you can use the remote terminal you have launched as instructed above.

To learn all you need about Unix operating system and its most basic commands you can work through the introduction and the first two tutorials of the [http://www.ee.surrey.ac.uk/Teaching/Unix/unix1.html online course] at the University of Surrey. If you need a bit more practice and want to go more in deep in your knowledge of Unix environment, you can go through the following [https://imperialcollegelondon.box.com/s/ogisiab652youex2jrgt2rrv7pr7u30m Unix induction tutorial], developed by Dr. Giuseppe Mallia.

=== Calculations ===

When you feel confident with using basic Unix commands (e.g. pwd, cd, ls, cp, mv), you can proceed (again via remote terminal) with running the calculations for the calculation of the adsorption energy of Hydrogen on different metal substrates.

To this end you will have to evaluate the energy of the clean metal slab <math>E_{surf}</math>, the chemical potential to bring Hydrogen from its reservoir (a Hydrogen molecule in gas phase) to the surface, <math>\frac{n}{2}E_{H_2}</math>, and the energy of the system where the hydrogen atom is adsorbed on the metal slab, <math>E_{surf +nH}</math>.

Having these numbers will make possible to evaluate the adsorption energy for Hydrogen on the metal

<math>\Delta E = \frac{1}{n}(E_{surf +nH}-E_{surf}-\frac{n}{2}E_{H_2})</math>

<math>n</math> is the number of H atoms adsorbed on the surface. In our case <math>n=1</math>

----

Steps:

----

'''1.''' You can download all the input files to carry out your calculations by doing wget https://github.com/ImperialCollegeLondon/VolcanoPlot/archive/main.zip If you wish, you can also download them on your computer https://github.com/ImperialCollegeLondon/VolcanoPlot/archive/main.zip as a .zip [https://github.com/ImperialCollegeLondon/VolcanoPlot/archive/main.zip file], but this is not needed to run the calculations on our cluster. Please avoid to save the zip file in a folder tree, where a folder has a name with one or more space (" ").You will see that you will have downloaded a file, main.zip, which you will unzip doing

> unzip main.zip

This will generate a folder named VolcanoPlot-main, containing among others, a tar file comp-lab.tar. You need to go to this directory and untar the comp-lab.tar file:

> cd VolcanoPlot-main
> tar -xvf comp-lab.tar

Once untared you will find there are several directories. You will to focus initially on:
*Pt Mo Ag Au: Directories with the input files to evaluate the energy of the metal surfaces and the energy of the metal surface with a H atom adsorbed on it.
*H2: directory with the input files to evaluate the energy of the hydrogen molecule
*files: folder containing the basis set and potential files,needed to run the CP2K calculation. Please keep them in this location

'''2.''' Go to project folder named as the metal surface it represents. For example, for platinum you will have to write:

> cd Pt

in that folder, you will find two subfolders, named as 'METAL' and 'METAL-H'.
You will be able to list these folders doing:

> ls

The folder 'METAL' and 'METAL-H' contain three files each: cp2k.inp, job.pbs and Struct_in.xyz, needed to run the code for the calculation of energy and relaxed atomic structure of the metallic surface under consideration.
In particular, cp2k.inp is the input file with the simulation parameters;
Struct_in.xyz contains the Cartesian coordinates for the atoms in your system;
job.pbs is the script that you will need to submit to run your calculation (see instruction below).
You will be able to list them them by doing:

> ls METAL/
or
> ls METAL-H/

'''3.''' go to one of the subfolders (you may start from the subfolder named METAL)and submit the calculation by doing

> qsub job.pbs

'''4.''' check the status of the job by doing:
> qstat

If the job is correctly submitted you will get some information about the number identifying you job (Job ID), the specific 'Class' of calculation, the name assigned to this job (Job Name), the status of your job (it could be running, or queued (Status) and additional comments related to the starting time of your simulation (Comment). Do not worry if the starting time of your simulation is not very close. This information is not final.

'''5.''' Take note of the Job Name and the corresponding running directory (the absolute path for your calculation may be something similar to:

/rds/general/user/[YOUR USERNAME]/home/VolcanoPlot-main/[SYSTEM]/[METAL, METAL-H or MOLECULE]/)

'''6.''' Wait until the job is finished. You do not need to stay in this directory. You can now go to the other subfolder (if you started from the subfolder named 'METAL' can now do

cd ../METAL-H

and do the steps 2 to 4 to submit another calculation.

'''7.''' Once you have submitted the calculations in 'METAL' and 'METAL-H' for the first metal, you can run the calculations for the other metals and for the H molecule, repeating steps 2 to 6.

'''8.'''Check from time to time if your calculations are still running by doing

> qstat

If you see that a calculation is not running anymore (its JOB ID will have disappeared from the qstat list), it might mean that the calculation is complete.

'''9.''' Go to the directory where the calculation was running. You will see there several files. The most relevant for you are:

*log.out is the main output of your simulation, with information about the convergence of the SCF cycle and
*Volcano-pos-1.xyz is the trajectory file with all the the geometry steps.
*Volcano-RESTART.wfn contains the wavefunctions for your system.

Now copy the files cp2k.inp, log.out and Volcano-pos-1.xyz for Pt METAL-H system and edit them:

What do you observe editing the cp2k.inp file? Can you tell
**what is the basis set used?
**what kind of calculation did you perform?
**what is the target accuracy for force calculation?
**what is the target accuracy for the SCF convergence?
**can you extract from the input the lattice parameters for your supercell?
**Is this an orthorombic cell?
**how many atoms do you have in your system?
**what is the hydrogen coverage in your system?

What do you observe editing the log.out file?
*How many self consistent cycles to converge for every geometry optimization step?
*what is the number of electrons and the number of occupied orbitals in your system?
*Did your calculation converge?

To extract the final energy corresponding to the optimised structure for your system you will have to do:

> grep "ENERGY| Total FORCE_EVAL ( QS ) energy (a.u.):" log.out.

After that, record the last line of the output. So, for instance, if you are analysing the energy of a metal surface where a H atom has been adsorbed, you will get <math>E_{surf+nH}</math>; if you are analysig the energy of a clean metal surface, you will get <math>E_{surf}</math>

'''10.''' Repeat point 9 for all the systems you have simulated and make a table with the measured exchange currents <math>i_0</math> as per table below and Hydrogen chemisorption energies for all systems.

[[File:Currrent.png|400px|thumb|centre|From Journal of The Electrochemical Society, 152 (3) J23-J26 ~2005]]

Now make a plot of the exchange currents <math>i_0</math> versus free energy for Hydrogen adsorption.

Do you see a Volcano? If yes, please fit the left and right part of it with two straigth lines and create a picture.
This is the main picture of your report.

Based on your volcano plot can you tell which metal is the best catalyst for Hydrogen evolution and why?

----

in this part of the experiment you will:

'''1.''' evaluate the error on energy and energy differences associated to the selection of some of the simulation parameters such as kpoints and basis set.

'''2.''' evaluate the equilibrium lattice parameter for all the metals you have studied.

'''1.'''
* you will first evaluate the error on the total energy associated to the Monkhorst-Pack k point set used to describe the Pt surface.
To this end you will have to calculate the total energy of your Pt surface using different k point grids (with a density ranging from 3 3 1 to 15 15 1) and evaluate the differences in total energy with respect to the most accurate set used. Please note that we assume that the (15 15 1) set samples the Brillouin zone accurately enough to be considered our exact reference total energy.

To do this, you will need to untar the file kpoints_unitcell-input.tar you have downloaded with wget. Once done, you will need to run the script kpoints_inputs.sh, by doing:

> ./kpoints_inputs.sh

This will create a separate input directory for every k point set and submit a calculation from every directory. Just test that you have actually submitted all the calculations by using the qstat command.

Once all your calculations converge, please plot a graph of the energy versus the density of the Monkhorst-Pack grid used; The zero of the energy scale in this graph should be represented by the value of the energy calculated with the most accurate k point set. Please, create a figure with this trend and and include it in your report.
What do you observe?

* you will then study the dependence of Hydrogen chemisorption energies on k-points set and basis set used to describe a 2x2 Pt slab with three layers. Two sets of data are included in the files Pt-kpoints-2x2.tar.gz and Pt-basis-2x2.tar.gz, fot slabs with 1/4 and 1 ML H coverages.
Please create vith VMD a picture with the surface and create picture for the above trends.
**What do you observe? How the error in the evaluation Hydrogen chemisorption energy versus kpoint and basis sets compares with the error in the evaluation of total energy in this system?

'''2.'''
* You will finally evaluate the equilibrium lattice parameters and bulk moduli for Ag, Au, Pt and Mo by fitting the energy versus Volume curve using the [https://en.wikipedia.org/wiki/Murnaghan_equation_of_state Murnagghan equation of state]. These data are contained in the bulk_modulus.tar.gz file. For each system, the enegy associated to 15 Volumes around the equilibrium Volume have been calculated. To fit these points and find the equilibrium lattice parameter please use the murn-new.x executable and do

> murn-new.x <in >lattice.out
> grep -A3 "alat=" lattice.out

You will find in this way the value for the equilibrium lattice parameter and bulk modulus. For one representative system plot a graph showing how the total energy varies with the cell volume.
How the obtained values compare with experiments?

Please check the materials databases
[https://www.materialsproject.org/ materials databases]
[http://www.aflowlib.org/search/advanced.php aflow library]

Finally, untar the relaxation trajectory for Pt slab contained in the file Pt-H-relaxation.tar.gz and visualise with VMD.
*what do you observe?

=== Structure of the experiment ===

Try to learn to use the Unix environment by Monday at the latest, to have submitted all the calculations by Tuesday at noon and to have finished to run all the calculations by Thursday. It will take time to analyse the results and understand all the new concepts that you will learn in this lab. You should be able to complete your experiment and to write your report by Friday.

Please note that the queueing system of our hpc cluster sometime doesn't allow to predefine the time when a calculation will run.
'''If your calculations won't have finished to run by Thursday morning, the relevant output files to proceed with the analysis will be provided on Thursday morning.'''

===Detailed timefame===

Monday (morning session): '''10:00 - 11:00 am: Short introduction to the experiment + Unix induction tutorial'''. Practise the use of Unix environment and its most basic commands.

Monday (afternoon session): '''2:00-2:30 pm short practical introduction to the steps to carry out in the the experiment'''. Submit your calculations and analyse your files.

Tuesday (morning session): '''10:00-11:00 am Theoretical lecture'''. Analyse your files and start studying trends.

Tuesday (afternoon session):Analyse trajectories; Study trends.

Thursday (morning session): '''10:00-11:00 am: Theoretical lecture + short VMD tutorial'''. Checkpoint for progress. Visualise your output with VMD.

Thursday (afternoon session). Study trends. Evaluate error. Create the Volcano plot.

Friday (morning session): Study trends; report write-up;

Friday (afternoon session): report write-up.

== Previous years related contents ==

- Python

- Thermodynamics

- Electrochemistry

Good skills on Unix operating system is not a requirement. All the scripts are written in a way where you only need to submit the script executing the commands. However, feel free to edit and play with the scripts.

== New contents ==

* Unix operating system

* Structural optimizations

* Periodic boundary conditions

* Evaluation of adsorption energies

* Volcano plots and Sabatier principle

== Submission of the report ==

You will need to submit
*The report as a PDF document, via Turnitin in Blackboard.
* all the input and output files you produced in your calculation via Blackboard, as a .zip folder.
'''
Please note that the submission boxes on Blackboard will appear only once you have completed
the curriculum review.'''

=== Write up ===

The report structure will consist of three sections:

* Introduction/Summary (Half-page)
* Questions & answers (No page limit)
* Conclusions (Half-page)

Tips to write a report:
* The golden rule: Aim for clarity
** Structured statements that flow in a logical manner.
** Good use of diagrams and appropriate level of theory.
** Careful choice of content.

* Keep your language clear and simple.
* Label all tables and figures. Labels should be self-contained, which means that tables and figures should be interpretable by themself.
* Appropriate referencing of figures and tables.
* Cite previous works (with an accepted citation style) whenever is appropriate.

Introduction/Summary:
* The purpose of the Introduction/Summary is to put the reader in the context of the experiment and to explain how the experiment was carried in the lab. It may contain a brief review of previous research, why the research was undertaken, an explanation of the techniques and why they are used and why it is important in a broader context.

Questions & Answers:
* There are a number of questions in the lab script that need to be answered in this section of the report.
* Depending on the nature of the question, it might be appropriate to use figures or tables to give a proper answer.
* It is highly encouraged to rationalise the answers.

Conclusions:
* The Conclusions gives a general description of the results and findings and it should be related back to the Introduction. If appropriate, suggest improvements or additional experiments.

=== Mark Scheme ===

The break-down for the marks for this lab are as follows:

{|class=wikitable
|-
|Introduction/Summary
|20%
|-
|Questions & Answers
|60%
|-
|Conclusions
|20%
|}

=== Plagiarism ===

Submissions are checked for plagiarism. External images may be used if correctly cited, but it's always better to create your own.

== Demonstrators ==

The demonstrators will be Dr Yueyu Zhang and Ms. Margherita Buraschi. They will be available via Microsoft team channel [https://teams.microsoft.com/l/channel/19%3ad0b2cfbabd994931bf16dd1435472e58%40thread.tacv2/comp_lab__catalytic_activity?groupId=577dc55a-ed12-45f5-b092-dfa9e184e14b&tenantId=2b897507-ee8c-4575-830b-4f8267c3d307 link Teams].
Feel free to contact them at the times specified above.

Outside the time in which the demonstrators are available,
all your questions should be posted in the forum on blackboard.

== Related literature ==

*W. Schmickler and E. Santos, Interfacial Electrochemistry, 2nd Edition, Springer
*P. W. Atkins Physical Chemistry, Oxford University Press (one edition of your choice)
*Psi-k Scientific Highlight of the Month. Theory of solid/electrolyte interfaces, Axel Gross, Univerisy of Ulm
*R. Martin, Electronic structure : basic theory and practical method - Cambridge, UK ; New York : Cambridge University Press 2008 - ebook available in the library.
*Nørskov, Jens Kehlet; Bligaard, Thomas; Logadottir, Ashildur; Kitchin, J.R.; Chen, J.G.; Pandelov, S.;
Stimming, U., Trends in the exchange current for hydrogen evolution, Journal of The Electrochemical Society, 152 (3) J23-J26 (2005)
*Allen Tildesley, Computer Simulations of Liquids, Oxford University press (2009).

== VMD and Periodic Boundary Conditions ==

On Thursday 2pm there will be a lecture about visualization of atomic structures with of VMD and the role of Perodic Boundary Conditions.

VMD is a visualisation programme which will make possible to visualise among other things,
the atomic structure of your surface and the cell used to represent it.
and create pictures with them.

To download VMD visualiser follow this [https://www.ks.uiuc.edu/Development/Download/download.cgi?PackageName=VMD link]
for Version 1.9.3 (2016-11-30) Platforms: Windows OpenGL (Microsoft Windows XP/Vista/7/8/10 (32-bit) using OpenGL)

You will need to register. Registration is free.

== Winscp ==

Winscp can be used to transfer files from and to the hpc platform to and from your computer.

To download winscp you will need to follow this [wincp https://sourceforge.net/projects/winscp/ scp link]

== Alternative instructions for Remote Connection ==

Please check with the demonstrators first.

if you are not able to connect to our hpc cluster using your browser or you could not install on your computer VMD or winscp:

# connect to an Imperial computer following this [https://remoteaccess.labstats.com/imperial-college-london Imperial remote access link]

You will need to follow the instructions and use your username and password.

Once connected you will launch Imperial Apps Anywhere , looking for https://softwarehub.imperial.ac.uk/ in your browser,
and look for winSCP and VMD therein.

# Click on the link in the email with subject "Register for Lab - IC_Chemisty_yr3_UK".

You can download files to your computer via command line opening a Linux terminal (or a terminal emulator) on your personal computer.

To this end you can follow this [https://www.doc.ic.ac.uk/~nuric/teaching/remote-working-for-imperial-computing-students.html link]