How to Calculate Adsorption Energy using Quantum ESPRESSO and DFT? [TUTORIAL]
Summary
TLDRIn this Phys Whiz tutorial, Manas Sharma demonstrates how to calculate the adsorption energy of a water molecule on the LiH (001) surface using Density Functional Theory (DFT) with Quantum ESPRESSO. The process involves three separate DFT calculations for the total system, the isolated molecule, and the surface. Sharma guides viewers through the use of BURAI, a GUI for Quantum ESPRESSO, to set up and run simulations, aiming to reproduce a study's adsorption energy value. The tutorial concludes with a comparison of the calculated energy to a reference value, highlighting the importance of pseudopotentials and energy cutoffs in achieving accurate results.
Takeaways
- šØāš« The tutorial is presented by Manas Sharma from Phys Whiz, focusing on calculating the adsorption energy of a molecule on a surface using density functional theory (DFT) and Quantum ESPRESSO.
- š§ The specific molecule and surface discussed are H2O (water) and the LiH (001) surface, respectively.
- š Adsorption energy is calculated using a formula that involves the total energy of the system and the energies of the isolated components.
- š A negative adsorption energy indicates favorable adsorption, although some literature uses a reverse convention with a positive value indicating favorability.
- š The tutorial references a 2017 paper and uses its supplementary material for the H2O-LiH system structure.
- š§© The structure provided includes various supercell sizes, but the tutorial uses the one with 16 Li and 16 H atoms, totaling 32 atoms in the surface.
- š The structure is converted into a CIF file for use in Quantum ESPRESSO, as opposed to the original VASP format (POSCAR file).
- š¬ The DFT calculation uses the PBE exchange-correlation functional aiming to reproduce the adsorption energy value reported in the paper.
- š Three separate calculations are needed: one for the total periodic system, one for the isolated H2O molecule, and one for the isolated LiH surface.
- š ļø BURAI, a GUI for Quantum ESPRESSO, is used to run the simulations and manage the project.
- š§ Pseudopotentials are carefully selected for each atom to ensure consistency and accuracy in the simulations.
- āļø Energy cutoffs and charge cutoffs are set, with occupations fixed due to the likely semiconductor or insulator nature of the materials.
- š¢ The tutorial demonstrates how to extract and calculate the final adsorption energy, comparing it to the value obtained in the referenced paper.
- š Links to the paper, simulation files, and a web app for unit conversion are provided in the description for further reference.
Q & A
What is the main topic of the tutorial presented by Manas Sharma in the Phys Whiz video?
-The main topic of the tutorial is calculating the adsorption energy of a molecule, specifically H2O on a LiH (001) surface, using density functional theory and Quantum ESPRESSO.
What is the general formula for calculating adsorption energy as described in the script?
-The general formula for calculating adsorption energy is the total DFT energy of the system minus the sum of the energies of the isolated molecule and the surface or slab.
What does a negative adsorption energy value indicate according to the convention used in the script?
-A negative adsorption energy value indicates that the adsorption is favorable, according to the convention used in the script.
What is the significance of the paper from 2017 mentioned in the script?
-The 2017 paper is significant because it provides the method and formula used for calculating the adsorption energy, and the script aims to reproduce the results from this paper using Quantum ESPRESSO.
How many atoms are in the surface structure used for the tutorial, and what is the total number of atoms including the H2O molecule?
-The surface structure used in the tutorial contains 32 atoms (16 Li and 16 H atoms), and including the H2O molecule, the total number of atoms is 35.
What is the purpose of using the same pseudopotentials for all atoms in the calculations?
-Using the same pseudopotentials for all atoms ensures consistency and accuracy in the calculations, preventing discrepancies that could arise from using different types of pseudopotentials.
Why is the energy cutoff for the wave function set to 50 Rydbergs and the charge cutoff to 500 Rydbergs in the calculations?
-The energy cutoff is set to 50 Rydbergs and the charge cutoff to 500 Rydbergs to ensure a balance between accuracy and computational speed, as a smaller cutoff speeds up simulations.
What is the role of BURAI in the calculations described in the script?
-BURAI is a GUI for Quantum ESPRESSO, and it is used to set up, run, and manage the SCF calculations for the total system, the isolated H2O molecule, and the isolated LiH surface.
What is the importance of ensuring that the water molecule does not interact with its neighboring periodic images in the isolated H2O calculation?
-Ensuring that the water molecule does not interact with its neighboring periodic images is important to accurately calculate the energy of an isolated molecule, avoiding any artificial interactions that could skew the results.
How does the script address the difference in conventions between a positive and a negative adsorption energy value?
-The script acknowledges that some papers use a reverse convention where a positive adsorption energy value indicates favorable adsorption. It clarifies that the results should be compared based on the magnitude, regardless of the sign.
What is the final calculated adsorption energy value in milli electron volts, and how does it compare to the value from the 2017 paper?
-The final calculated adsorption energy value is -223 milli electron volts, which is close to the value of 219 milli electron volts obtained in the 2017 paper, indicating good agreement despite slight differences.
What could be the reasons for the slight difference between the calculated adsorption energy and the value from the 2017 paper?
-The slight difference could be due to different choices of pseudopotentials or the energy cutoff not being fully converged, suggesting that a larger or smaller value might have been used in the paper.
Outlines
š¬ Calculating Adsorption Energy with DFT and Quantum Espresso
In this tutorial, Manas Sharma introduces viewers to the process of calculating the adsorption energy of a molecule on a surface using Density Functional Theory (DFT) and the Quantum Espresso software. The specific example given is the adsorption of a water molecule (H2O) on the LiH (001) surface. The adsorption energy is determined by calculating the total energy of the system and subtracting the energies of the isolated components. The tutorial emphasizes the importance of understanding different conventions for calculating adsorption energy, where a negative value can indicate favorable adsorption in one convention, while a positive value does in another. The structure of the H2O-LiH system is sourced from a 2017 paper, and the tutorial aims to reproduce the adsorption energy value reported there using the PBE exchange-correlation functional.
š Preparing Quantum Espresso Simulations with BURAI GUI
The second part of the tutorial focuses on setting up simulations using the BURAI graphical user interface (GUI) for Quantum Espresso. The process involves assigning pseudopotentials to each atom in the system, ensuring consistency and choosing pseudopotentials with a smaller energy cutoff to speed up simulations. The tutorial explains the importance of selecting the appropriate energy and charge cutoffs and using fixed occupations for the material, which is likely a semiconductor or insulator. The calculations for the total system, the isolated LiH surface, and the isolated H2O molecule are prepared, each with specific settings for wave function and charge cutoffs, and occupations. The tutorial also details the steps to run the self-consistent field (SCF) calculations for each system.
š Analyzing Results and Comparing with Literature Values
In the final segment, the tutorial demonstrates how to analyze the results from the Quantum Espresso simulations. The energies obtained from the calculations for the total system, the isolated LiH surface, and the H2O molecule are extracted and used to calculate the adsorption energy. The process includes using an online calculator to convert the final adsorption energy from Rydbergs to electron volts. The calculated adsorption energy is then compared with the value reported in the literature, noting that the results are in good agreement despite minor differences that could be attributed to different pseudopotential choices or energy cutoff values. The tutorial concludes by summarizing the steps taken to calculate the adsorption energy and encourages viewers to like, subscribe, and comment with any questions or doubts.
Mindmap
Keywords
š”Adsorption Energy
š”Density Functional Theory (DFT)
š”Quantum ESPRESSO
š”Pseudopotentials
š”SCF Calculation
š”BURAI
š”CIF File
š”Supercell
š”Gamma Point
š”Occupations
š”Rydberg
Highlights
Introduction to the tutorial on calculating adsorption energy using density functional theory and Quantum ESPRESSO.
Explanation of adsorption energy and its significance in understanding the interaction between a molecule and a surface.
The formula for calculating adsorption energy and the implications of a negative value indicating favorable adsorption.
Different conventions for calculating adsorption energy and their impact on the interpretation of results.
Selection of the H2O-LiH (001) system for the tutorial and the importance of choosing an appropriate system.
Use of supplementary material from a 2017 paper to obtain the structure of the H2O-LiH system.
Conversion of the structure into a CIF file for use with Quantum ESPRESSO, emphasizing the importance of file format compatibility.
The choice of the PBE exchange correlation functional for the DFT calculations.
Targeting to reproduce a specific adsorption energy value from the literature using Quantum ESPRESSO.
Introduction of BURAI, a GUI for Quantum ESPRESSO, and its role in simplifying the simulation process.
The necessity of running three separate SCF calculations for the total system, isolated molecule, and isolated surface.
Importance of selecting appropriate pseudopotentials for accurate simulation results.
Setting energy and charge cutoffs in BURAI to optimize simulation speed and accuracy.
Preparation of inputs for the isolated LiH surface calculation, emphasizing the need to remove the H2O molecule from the structure.
Ensuring the isolated H2O molecule does not interact with its periodic images by adjusting the unit cell size.
Execution of SCF calculations for each system component and the importance of using the same pseudopotentials across calculations.
Extraction of total energy values from the results and the process of calculating the final adsorption energy.
Comparison of the calculated adsorption energy with the literature value and discussion of potential reasons for discrepancies.
Conclusion of the tutorial with a summary of the steps involved and the outcome of the adsorption energy calculation.
Encouragement for viewers to like, subscribe, and ask questions for further engagement with the content.
Transcripts
Hey guys, how's it going? I'm ManasĀ Sharma and welcome back to Phys Whiz.
In this tutorial, I'll be showing you guysĀ how to calculate the adsorption energy of aĀ Ā
molecule on top of a surface using densityĀ functional theory and quantum espresso.
Now for this tutorial, we'll beĀ calculating the adsorption energyĀ Ā
of the H2O or the water moleculeĀ on top of the LiH (001) surface.
And the adsorption energy is usually givenĀ by a formula that looks something like this.
So you basically calculate the energy, the DFTĀ energy of the total system, total periodic systemĀ Ā
and then you subtract the energies of theĀ isolated molecule or in this case the waterĀ Ā
molecule as well as the slab or the surface,Ā that is in this case the LiH (001) surface.
So you calculate the total energyĀ and then you subtract the energyĀ Ā
of the components from it and thisĀ gives you the adsorption energy.
And please bear in mind that if youĀ use this formula or this convention,Ā Ā
then a negative value of the adsorption energyĀ indicates that the adsorption is favorable.
However, some you know scientists or papers alsoĀ use a reverse formula or reverse convention.
For example, if we go to this paper here, thenĀ they use a formula where they subtract theĀ Ā
energy of the total periodic system from theĀ sum of the components and in this conventionĀ Ā
a positive value of the adsorption energyĀ indicates that the adsorption is favorable.
So just keep this in mind whenever you'reĀ calculating or comparing your results withĀ Ā
literature and umm, so we will be followingĀ this paper, umm for this particular tutorial.
This paper was written back in 2017 and weĀ will obtain the structure of the H2O-LiHĀ Ā
surface from the supplementaryĀ information of this material.
Now I have already downloaded theĀ supplementary information and theyĀ Ā
have provided the coordinates of the H2OĀ LIH system of various supercell sizes.
So they provide, you know, systemsĀ where you have 16 atoms in the surface,Ā Ā
32 atoms in the surface, 64 atomsĀ and 128 atoms in the surface.
Now for this tutorial to keep it quick, we'll beĀ using the second structure that contains 16 LiĀ Ā
and 16 H atoms, giving us a total of 32 atoms inĀ the surface and three atoms of the H2O molecule.
And I have already converted this structureĀ into a CIF file as you can see over here.
So they provided it in the VASPĀ format that is a poscar file.
But here is a CIF file and forĀ this tutorial what we will beĀ Ā
doing is we will be calculating the DFTĀ adsorption energy using the PBE exchangeĀ Ā
correlation functional and tryingĀ to reproduce this particular value.
So in this table two of this paperĀ they calculate the adsorption energyĀ Ā
using a gamma point and 32 atoms in theĀ surface which is what we are also using.
And with PBE they get an asorptionĀ energy of 219 milli electron volts.
And in our convention, it would actually be -219Ā electronvolts, but that really doesn't matter.
What matters is the magnitude.
So let's see if we can reproduce this valueĀ with Quantum Espresso in our simulations.
Now to run the Quantum Espresso simulations,Ā Ā
I'll be using BURAI, which is GUI forĀ Quantum Espresso that I really like.
And in order to calculate the adsorption energy,Ā Ā
we'll need to run 3 calculations,Ā 3 SCF calculations actually.
So first will be the energy SCFĀ calculation on the total periodic system.
The other would be for the isolated H2O molecule,Ā Ā
and the last would be forĀ the isolated LiH surface.
So let's come back to BURAIĀ and import this CIF file thatĀ Ā
I already have and I'll put itĀ in the description down below.
And in fact, I'll put the link to theĀ paper as well as all the simulationĀ Ā
files that we create in this tutorialĀ will be in the description down below.
So please be sure to check it out.
So let's import this structure into BURAI.
Now it looks really good and so nothing seems odd.
However, what we'll have to check is ifĀ the pseudo potentials are correct or not.
Now you can see that BURAIĀ has assigned pseudopotentialsĀ Ā
of different categories to each atom.
So let's be consistent andĀ assign the same category.
Or you know the type of the pseudo potential toĀ be PAW for each of the atoms, so I'll choose.
Let's say this one.
Which is a PAW pseudo of potential I IĀ am not choosing this one because here theĀ Ā
cutoff of the wave function is reallyĀ high, that is 102 oryeah, 2 rydbergs.
But I'll use this one because here theĀ cutoff, the energy cutoff is quite small.
So this actually, you know,Ā Ā
speeds up your simulations if youĀ have a smaller cutoff of energy.
So let's choose this pseudo potential for Li now.
Similarly, let's choose a PAWĀ potential for hydrogen atom.
And again, for oxygen, let's.
Choose PAW pseudo potentials such as this one.
Now you can see in all these pseudoĀ potentials that we have chosen theĀ Ā
cutoff of the recommended cutoff for theĀ energy is never more than 49 Rydberg.
So this should keep our simulations fast.
Now let's go ahead and save this projectĀ and call it H2O-Li16H16 and save it andĀ Ā
then come to the SCF tab of BURAI and here weĀ will write the cutoff to be 50 rydbergs and.
To be safe, we will set the cutoffĀ for charge to be 500 rybergs.
That is 10 times of 50.
And we will use fixed occupations because thisĀ is probably a semiconductor or an insulator.
So let's just go ahead and save this project onceĀ again and run the SCF calculation on 4 threads.
OK, now while this is running, let's also prepareĀ the inputs for the other two calculations.
That is the isolated LiH surface.
So once again, just import this CIF file.
Into BURAI and this time weĀ will delete these three atomsĀ Ā
corresponding to the water molecule,Ā so they are at the end of our file.
So we will just go aheadĀ and delete all these three.
Atoms and this just gives us theĀ LiH-001 surface. Now once againĀ Ā
we will come to the elements tab to setĀ our pseudopotentials and we will againĀ Ā
choose the same paw pseudopotentialsĀ that we chose for the total system.
And let's now save thisĀ project by the name Li16H16.
Again, come to the SCF tab and set theĀ cutoff for wave function to be 50 rydbergs.
Charge to be 500 rydbergs;Ā occupations to be fixed.
And by the way, I didn't mentionĀ it but we are using just a gammaĀ Ā
point here because we are trying to reproduce thisĀ Ā
value in the paper and this was alsoĀ obtained using a gamma point calculation.
So we are just using that.
So let us save it again and run the SCFĀ calculation for this particular system as well.
Using 4 threads again, so we we canĀ see that the previous calculation isĀ Ā
still running while the newerĀ calculation is in the queue.
And in the meanwhile, let's prepare the.
Calculation for the third energy SCF calculation.
That is for the isolated H2O molecule.
So let's import the CIF file into a BURAI againĀ Ā
and this time we will getĀ rid of all the LiH atoms.
So just go ahead and selectĀ all these and get rid of these.
And then upload this to the GUI.
OK so that works.
However this time I'm goingĀ to make one more change so.
Since this calculation has to be for anĀ isolated water molecule, we need to makeĀ Ā
sure that the water molecule doesn't interactĀ with its neighbouring periodic images and I'mĀ Ā
not sure if you know this particular unitĀ cell or supercell with would do the job.
So let me switch to a cubic unit cell with youĀ know lattice parameter of 15 angstrom and thisĀ Ā
would definitely make sure that the water moleculeĀ is not interacting with its periodic images.
Again, we will set the sameĀ pseudo potential that we usedĀ Ā
before because this is really important,Ā otherwise your results won't Make sense.
So let's use the paw again and save this projectĀ by the name H2O and come to the SCF tab again.
And this time again, we will choose theĀ same energy cutoff and charge cutoff.
And this time again this wouldĀ be gamma point calculation,Ā Ā
because for molecules the KĀ points don't really make sense.
Set the occupations to fixed for molecule,Ā Ā
save it again and run the SCFĀ calculation for this system as well.
OK, so now let's see.
OK, so now we can see that the previousĀ two calculations have already finished,Ā Ā
so let's go ahead and extract the energy.
So here we will go to results.
And see the log file.
Search for the final total energy and here it is.
So the final total energy at the end is this.
So let's go ahead and copy this.
Copy and then come to our browser,Ā let's say or calculator, whatever.
I'll be using Wolfram Alpha actually.
And I'll paste this value over here.
Sorry, something went wrong, OK.
Copy and paste this value overĀ here and so this would be theĀ Ā
value for the energy value for the total system.
Then we will subtract theĀ energy of the components.
So let us now go ahead and pickĀ up the energy for the slab.
So again in the results log fileĀ search for the total energy.
That is over here.
Go ahead and copy this.
And again, paste it over here and I believeĀ Ā
that the calculation for the H2OĀ molecule is also converged now.
So let's go ahead and check that out.
Log file search for this exclamation mark.
And actually this is still running,Ā so let's just wait for a few minutes.
OK? So now it's done.
So, OK, so now it is finished and we'll justĀ Ā
go ahead and copy this energyĀ again and paste it over here.
And let's see what we get.
So we get an adsorption energy that is negative soĀ that it negates that the absorption is favorable.
Do not worry if it is not positive becauseĀ this paper was using a reverse convention.
So basically our results are equivalent.
Right now both results indicate that theĀ Ā
adsorption is favorable and weĀ get a value of 0.0164 Rydberg.
So let's calculate that and come to this web appĀ Ā
that I have created and convert thisĀ value in Rydbergs To electron volts.
So paste in this value inĀ Rydbergs and here is what we get.
So our result is that the adsorptionĀ energy is -223 milli electron volts.Ā Ā
And don't worry about the minus sign. As IĀ already mentioned the arc convention is theĀ Ā
opposite so these two results are equivalentĀ and our results results of 223 Milli electronĀ Ā
volts is actually quite close to the resultĀ obtained in this paper of 219 Milli electronĀ Ā
volts using VASP and the remaining differences,Ā In our results could be due to various facts.
So one reason could be a differentĀ choice of pseudo potential.
I'm not sure what pseudopodential did they use.
Another reason could be I didn't really convergeĀ my results with respect to the energy cut off.
So maybe 50 rydbergs wasn't enough.
Maybe I should have chosen a largerĀ value, maybe they chose a smaller value.
So these could be the reasonsĀ for this very slight difference.
But overall I think this is a reallyĀ good agreement with the reference.
So yeah, so that is it.
In today today's tutorial, you have learnedĀ how to calculate the asorption energy of aĀ Ā
molecule on top of the surfaceĀ using Quantum Espresso and DFT.
I hope you guys really enjoyedĀ this tutorial and found it useful.
In case you did, then don't forget to hitĀ Ā
the like button and subscribe to myĀ channel for more videos like this.
If you have any questions or doubts, leaveĀ them in the comment section down below.
And thanks for watching.
Have a great day.
Browse More Related Video
MSE 201 S21 Lecture 37 - Module 1 - Free Energy of Nucleation
A Level Chemistry Revision "Relative Molecular Mass and Relative Formula Mass"
Membuat Partikel Kuantum di Laboratorium (Quantum Dots)
What is The Schrƶdinger Equation, Exactly?
OXIDATIVE PHOSPHORYLATION | Cellular Respiration
Surface Area Analysis of Carbon Materials
5.0 / 5 (0 votes)