SCF Calculations using BURAI (GUI for Quantum ESPRESSO) - [TUTORIAL #4]

[@satomichinishihara3480]

Thanks for making interesting tutorials of my software :-)

[@PhysWhiz]

I should be thanking you for creating BURAI. Really grateful! :)

[@johnconrad4439]

Hello total newb here. I have a question: do scf and band calculations really take a long time? Like how long on the average? Im trying to do scf and band calculations for fcc fullerene (C60 so a total of 240 atoms) and its been 30 mins and burai still says calculating. Is this a hardware problem (unfortunately im only using a 4gb ddr3 ram with core i5 processor)? It wasnt this slow when I tried to do the same with the NaCN sample in the examples folder.

[@etiennepalos4319]

@@johnconrad4439 240 atoms? You're in for a long ride... hope it's done by now!

[@PhysWhiz]

@@johnconrad4439 The calculation time scales with the number of electrons, unit cell size, KEcutoff, etc. Moreover on just 4 GB RAM I think you can only run a serial calculation rather than a parallel one, which makes matters worse.

[@arpitamukherjee7363]

I am getting an error as Commands: "mpiexec.exe - n 4 pw.exe" while executing. Kindly help.

[@ivanocoatlguido1356]

It´s same to me, how fix this error? Thanks you.

[@hennamalakar2380]

I'm facing problem in running the file. It says error, command: pw.exe -in espresso.in . Can anybody help on this?

[@PaulGaurav]

This is Great! Thank you Phyz whiz.

[@kamalgurnani924]

Hello, this video was really helpful in understanding the usage of those parameters but could you please explain what exactly is ecutwfc physically and how increasing it causes the energy to converge? I must better ask what exactly does it put the cut-off on? I asked the latter question because there are ecutwfc, ecutrho and ecutfock, these all should not be the cut off for one variable 'energy', I think it is the cut-off for something else.

[@PhysWhiz]

ecutwfc and ecutrho are the kinetic energy cutoff of the plane wave basis used to describe the wavefunctions and the charge density, respectively. The larger the energy cutoff, the slower the calculation would be, but more accurate. The choice of the cutoffs depends only on the pseudopotentials you are using and on which quantities you are interested in (for instance, magnetic properties are harder to converge wrt total energy). Once you've chosen your PPs you can test convergence of the energy wrt to cutoffs in the cheapest system (usually in the bulk).

[@PhysWhiz]

"...when we make a Density Functional calculation with plane waves, the (electronic) wavefunction is represented as the infinite summation of plane waves, which must be truncated, in order to be able to handle them computationaly. So, the more plane waves, the more accuracy, but also higher computational cost. The trick for speeding up the calculations relies on the fact that the plane waves with less kinetic energy (represented as ℏ2 / 2 m |k+G|2) have higher contribution to the totality, so the plane waves with lower energy are the most important. But, up to which point should we increase the cutoff, so that we get a good balance between computational cost and accuracy? That is precisely the optimum cutoff choice." From blog.larrucea.eu/checking-optimum-cutoff-qe/

[@ShoaibMuhammad85]

Hi thank you for these nice tutorials :) It would be nice if you could make a tutorial on using Hubbard Parameter in BURAI or simply put a page on bagitoff page?

[@PhysWhiz]

Hi there, I know I'm a little late. But I wrote a blog post, a while back. Here I share my opinion on how one could go about the process. You can check it out here: www.bragitoff.com/2018/02/calcuate-hubbard-parameter-u-j-quantum-espresso-solved/ I should mention that I'm myself a beginner so I may not be a 100% correct. So I would appreciate your feedback on it.

[@HIRENP]

thanks for such nice information. but i want to know how to optimize k-points and lattice parameter, please upload video for that thank you

[@science.ashutosh]

Hello.. I am trying to do SCF calculation of MnO2. I dont know which potential is suitable for this. How to check it? Also there are three atoms in the unit cell. How long it should take to complete the calculation?

[@PhysWhiz]

Usually ultra-soft pseudopotentials are good for research puprposes. You can also try searching for research papers using QE and MnO2 and see what they used. With just 3 atoms in the unit cell, it shouldn't take too long. Maybe 10 minutes at max.

[@alexaku9918]

Help me please! I need to change integer and decimal separator in BURAI from comma to dot. BURAI opens all files with commas by default. And QE doesn't run with this files.

[@shukurgofurov1989]

Sorry for simple question: I have a computer with 2 processors totally 24 cores (12+12) and 48 threads. When I run calculation default setting shows 48 and 1 for "processes MPI and Open mpi. Should I keep this setting?!

[@semontis]

This is a wonderful tutorial. However, while performing SCF calculations I faced the following error, "Failed to post close command error 1726" and "unable to tear down the job tree. exiting.." Have you faced anything like this? I found several people reporting this problem in the forum, but it is not resolved yet.

[@nazmussaadat1156]

Excellent and useful videos. Thanks. My question is if I want to rotate the layers of atoms (e.g., graphite) at different angles is there any option? I can see translational option, but not rotational. Appreciate your kind opinion

[@mmbytes1911]

Should i run scf file first then relax and then vc-relax or can run directly run vc-relax because every calculation takes much time, Please

[@ahsanulaudri4261]

ERROR: Failed to post close command error 1726 ERROR: unable to tear down the job tree. exiting... Can you please explain, how to run successfully,,,, every time when I save and then click run,,, the structure does not optimize and this error occurs...

[@shahranahmedjoy7637]

Hello! When I am trying to do the SCF calculation,an error occurs and this line occurs in the dialogue box ''mpiexece.exe -n 4 pw -in espresso.in'' Can you please suggest what should I do??

[@universe2973]

I am getting the same error... What u did?

[@karanshah9354]

@@universe2973 Try Number of MPI processes 1 and Thread MPI process as 4. In SCF tab, keep restart option No

[@karanshah9354]

@@neelusharma3391 Plz try above reply. It worked for me.

[@karanshah9354]

@@neelusharma3391 then Sorry. I hope the video tutor can help.

[@munishbattu]

how material API is working in Burai top right corner.when we search any material it say no API material data found.

[@fatimanovel5114]

Hi, hope you will be okay. No doubt your explaining style is Impressive. I have question about CoO SCF file run easily but in case of Co2O3 its carsh during in few second of running file.why it happen?what's solution? Kindly must reply

[@saleelahammad6034]

How can we get the volume of optimized structure

[@chinyereanyama1802]

You are doing really amazing. How can i access your first three videos?

[@PhysWhiz]

Glad you like them! Here is the playlist kzbin.info/aero/PLUhYFZgYOn8ejBZZqyK4LsjERNd7KtC8R

[@chamacesa]

Amazing bro... Tnx... =)

[@qammaralmas8915]

Thanks a lot!

[@raja0300100]

sir i faced some that i could not resolve please guide.. ERROR IN RUNNING THE PROJECT COMMAND:pw.exe-in espresso.in

[@divyasingh7215]

Hey, I am a newbie to QE. Could you upload a tutorial for VFE, IFE, NEB for migration of point defects calculations in metals using QE?

[@dianapradhan4633]

Hello.. Thanks for the nicely presented video. But for SCF calculation of MoS2 (which is not available at Material API), I followed the following steps and faced error as described below: 1. Downloaded the CIF file (1011286.cif) for MoS2 from crystallography.net website 2. Saved the CIF file inside examples folder of the .burai folder 3. Chose SCF as you showed in the video and clicked on RUN 4. Save the project by creating a new folder as "1011286" 5. After that it is showing ERROR in running the project: C:\Users itr\.burai\1011286\1011286 COMMAND: C:\Users itr\Downloads\BURAI1.3_Windows\BURAI1.3_Windows\exec.WIN\mpi\mpiexec.exe-n 4 C:\Users itr\Downloads\BURAI1.3_Windows\BURAI1.3_Windows\exec.WIN\pw.exe-in expresso.in 6. After going to result section, it shows these three files CRASH, IN, LOG.scf Can you please help me knowing where did I go wrong and how to correct the mistake.. It is very urgent. Thank you in advance.

[@PhysWhiz]

Hi there, could you please tell me whats written in Crash file and log file.

[@dianapradhan4633]

@@PhysWhiz task # 0 from read_cards : error # 1 species Mo4+ in ATOMIC_POSITIONS is nonexistent %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% task # 2 from read_cards : error # 1 species Mo4+ in ATOMIC_POSITIONS is nonexistent

[@omermutasim1200]

@@dianapradhan4633 make sure the spelling/small/capital of Mo4+ is consistent with name of atoms mentioned in ATOMIC_SPECIES card, i think you should also write the atom (Mo) instead of ion (Mo4+)

[@ammar2140]

excuse me, sir, so I'm doing research using qe burai, but when I run anything (optimize, scf, etc) the result is immediately goes green and it says 'fatal error in mpi_init_thread' in the LOG, I wonder why? , even though the placement of pw.x and mpi is correct. Thank You.

[@PhysWhiz]

Hi, The error can occur if there is something wrong with your input file. You will find more information about the nature of error if you go to Results-> log or CRASH file. There you will find the exact problem. The MPI error message is displayed even when the problem is related to the input file.

[@ammar2140]

Ok thank you for the reply, i also wondering if in BURAI quantum espresso, is it already have a method called d3 or dispersion built in?

[@PhysWhiz]

Based on the user guide, it does have dispersion correction but I am not aware about how to do it.

[@ThePhysicsGuruJi]

Hello sir, please tell me in which order data is written in espresso.pdos_atm#45(I)_wfc#2(p) file

[@fatimamahi7023]

I have a problem in installation of BURAI can you help me please.

[@bishalthapa4639]

how does k point defined for scf calculation, i found that the k point sample point are extensively define for scf cal. but for band structure calcualtion they are not?? apprecciated if you'd reply

[@PhysWhiz]

What do you mean by extensively defined?

[@vidyasaraswathimalla8359]

Hi sir. I am a beginner in this QE software. I would like to know the atomic magnetization value of Dysprosium

[@vivekpendharkar5152]

Hey I actually want to perform SCF calculations for Nickel FCC on BURAI however I'm not able to find the Ni file in the projects. Is there any place you know where I could find it?

[@zelenik.]

Crystallography Open Database

[@arunpalakkandy6717]

When I press Element tab of geometry, there is no pseudopotential listed, even though files exist in Burai1.3.2 directory and qe-7.0 directory. Cant seem to get the software to access it

[@PhysWhiz]

That is strange. Which OS are you using?

[@arunpalakkandy6717]

@@PhysWhiz I am on ubuntu 20.04. This problem I overcame when I realized there was a mistake in the path of QE. Now I am encountering a new problem, error file gives "error while loading shared libraries: libmpi_mpifh.so.12: cannot open shared object file: No such file or directory". I installed openmpi v1.10 which is supposed to have this file. locate command shows I have /usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_mpifh.so and ....so.40.20.2 but no so.12. Thinking of which, is there a Burai version which does not require multicore or multiprocessing? By the way thank you for your reply. Hope you can help here.

[@PhysWhiz]

Hi, unfortunately I could never get BURAI working 100% on Ubuntu or MacOS. It just doesn't play well for these two OS. I usually then use it as a structure modeling software and add the pseudopotential paths myself. Take the input file, and run it using my own compiled QE. It is quite easy to compile QE on Linux. There is a video on my channel for parallel version compilation.

[@arunpalakkandy6717]

@@PhysWhiz Got it. Maybe if Burai came with a version that doesn't need multi processors things would be better. I linked burai to QE that runs on command line. That too gave a multi-core error.

[@hinneschan8439]

I also tried to download Burai and work that way. It couldn't run at all and only said error running the project and showing the mpirun command line. I guess it'd better if a detailed error msg is given cos it is a superb and user-friendly tool.

[@Hunar1997]

Reduce the number of process and threads amd see if its working now

[@Bangalibabu95]

How do I apply electric field?

[@science.ashutosh]

What should i do when the energy is not converging even after 200 iteration?

[@PhysWhiz]

That usually means that the starting geometry is quite wrong. You also mentioned that the MnO2 unit cell has three atoms,. I am not sure what particular crystal system that is but wikipedia shows it as having like 8 atoms: 2 for Mn and 8 for O2. Maybe you're running on a primitive cell or something. But since your scf is also not converging its most likely an issue with your geometry. Can you provide some details regarding that here?

[@science.ashutosh]

@@PhysWhiz Yes. I have done the Rietveld refinement of the XRD pattern of alpha MnO2. From the refinement data I find three atoms: one for Mn and two for oxygen (different atomic position). I started with this and with pseudo potential but i am unable to complete the calculation.

[@PhysWhiz]

@@science.ashutosh what are the atomic positions and lattice parameters you got from that?

[@science.ashutosh]

@@PhysWhiz The atomic positions are like: Atom Ntyp X Y Z B occ. in fin Spc Mult B11 B22 B33 B12 B13 B23 Mn1 MN 0.32406 0.14210 0.50000 0.00000 0.42641 0 0 0 8 Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 O1 O 0.20124 0.12550 0.00000 0.00000 0.47018 0 0 0 8 Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 O2 O 0.51915 0.19711 0.00000 0.00000 0.58202 0 0 0 8 Codes: 0.00000 0.00000 0.00000 0.00000 0.00000 and lattice parameters are: Direct cell parameters: 9.8214 9.8214 2.8567 90.0000 90.0000 90.0000 Crystal system: Crystal System: Tetragonal

[@PhysWhiz]

I meant 6 atoms, 2 for Mn and 4 for O.

[@NavdeepSingh-jn9lb]

I am facing the error in running the project, pwe.exe -in espresso.in It fails to launch pwe.exe -in espresso.in on my PC. The system can't find the file specified. Plz, solve this problem

[@fatimazaggout4253]

i am facing the same problem pls show me how did you solve it if u have solved it

[@NavdeepSingh-jn9lb]

@@fatimazaggout4253 , somehow i got the results, but it is very difficult to explain here in comment section.

[@mekrajavel718]

@@NavdeepSingh-jn9lb Hii, I am also facing the same problem that you faced earlier. Can you please drop your email? I want to solve this problem. Thank you

[@hennamalakar2380]

@@NavdeepSingh-jn9lb hi, can you explain how you solved this because I'm having the same problem

[@sahirmalik859]

Plz tell me how we add more fingers on this because I need Nio crystals

[@priyankaroy6804]

Hello sir, thank you for making such videos. Can u please tell how to get bond length n angle using burai software. Please respond 🙏.

[@PhysWhiz]

Hi, unfortunately BURAI is not suitaboe gor analyzing the structural properties like bond lenghts or angles. For that you can check out my tutorials on VESTA. After modeling a structure in BURAI you can copy the coordinates and make an xyz file and then ooen it in VESTA to visualize and analyze the structure.

[@priyankaroy6804]

@@PhysWhiz Thank you so much sir🙏

[@sandeepbaral8383]

sir how to input 3C sic polytypes of sic crystal to calculate SCF using this software

[@hoseinghobadi2535]

I run the calculation same as you but in the result tab only appears the IN file, no LOG .scf. Any ideas?

[@PhysWhiz]

Are you using Windows or something else? For me BURAI only works on Windows.

[@hoseinghobadi2535]

@@PhysWhiz I am using windows

[@jm394]

I am not getting the log files or the convergence file at the results tab. I can only find the input file there. What am I doing wrong?

[@rishabhkaurav]

Actually currently I am facing the same problem... Could you please tell me what you did to resolve it.. thanks

[@jm394]

@@rishabhkaurav Sorry, it's been a while so I don't remember anything. I think in the end I could not even make this software work. Used Gaussian in the end.

[@rishabhkaurav]

@@jm394 okk thanks for making time to reply... Even I am thinking to dual boot Linux for this..

[@rockentech8113]

Can i use this software in PhD is it so relaible as wien2k

[@PhysWhiz]

I think yes. It has thousands of citations by very reputed researchers

[@hinneschan8439]

Hi, thanks for going through the tutorial in such a nice way. I tried to duplicate your settings and run using PWgui. However, my total energy converged to 553eV and bandgap of 6eV which are obviously not correct. What's wrong with it? here is the input file. &CONTROL calculation = 'scf' , max_seconds = 86400 , restart_mode = 'from_scratch' , outdir = '/home/edmund/Quantum-Espresso/Tutorial/tmp/' , pseudo_dir = '/home/edmund/Quantum-Espresso/pseudo/SSSP_Acc/PBE/' , prefix = 'si' , / &SYSTEM ibrav = 1, celldm(1) = 5.46873, nat = 8, ntyp = 1, ecutwfc = 44.000 , ecutrho = 440.00 , nbnd = 32, occupations = 'fixed' , nspin = 1 , / &ELECTRONS electron_maxstep = 200, conv_thr = 0.000001 , startingpot = 'atomic' , startingwfc = 'atomic+random' , mixing_beta = 0.7 , / ATOMIC_SPECIES Si 28.08550 Si.pbe-n-rrkjus_psl.1.0.0.UPF ATOMIC_POSITIONS angstrom Si 0.000000000 0.000000000 0.000000000 Si 4.101546000 4.101546000 1.367182000 Si 0.000000000 2.734364000 2.734364000 Si 4.101546000 1.367182000 4.101546000 Si 2.734364000 0.000000000 2.734364000 Si 1.367182000 4.101546000 4.101546000 Si 2.734364000 2.734364000 0.000000000 Si 1.367182000 1.367182000 1.367182000 K_POINTS automatic 4 4 4 0 0 0

[@anishdas39]

celldm(1) = 5.46873 ???, when your using celldm(1) kind of parameter, you should provide the unit of bohr

[@soumyakannoth1]

Iam not able to give GGA+U.. even if i give values it automatically becomes zero...what will be be the reason?

[@PhysWhiz]

Thats weird. Maybe you can try editing the value in input file and then press the up arrow icon in the top right of input file to make these values update in the GUI

[@PhysWhiz]

Also which version are you using? Maybe try using 1.3.2 which i thin is the latest as of now

[@soumyakannoth1]

@@PhysWhiz BURAI 1.3

[@sarojthapa3873]

Hi, I am new to this sort of calculation and try to duplicate the things as you have done in the videos, but it shows error "COMMAND: pw.exe-in espresso.in". Can you please help me to fix that? I am using it in windows 10.

[@PhysWhiz]

In the results section there must be a crash file. What does that say

[@universe2973]

I m getting the same error. In the result section it only shows IN option

[@karanshah9354]

@@PhysWhiz From pw_readfile : error # Error Opening XML data file

[@karanshah9354]

I switched restart option to No and now it works fine

[@PhysWhiz]

@@karanshah9354 I'm glad you figured it out and are trying to help others.

[@niyatishah7492]

I set all the parameters to the values you did, yet am still getting an error while running the project. Can you help me with that?

[@PhysWhiz]

What's the error?

[@niyatishah7492]

@@PhysWhiz it doesn't say. It just states my file destination and says error in running calculations

[@user-ck8md6gz9l]

I am facing problem on running the input file ' error in running the project'. If anybody there to help me out with this problem please let me know.

[@prajitvishnukarthik8886]

IT is showing SCF not convereged. waht can i do?

[@PhysWhiz]

There are several steps that can be taken to address convergence issues in DFT calculations using Quantum Espresso: 1. Try increasing the maximum no. of SCF iterations, in case you were close to convergence but not fully converged. 2. Check the quality of your input data, such as the crystal structure and the k-point grid. Inaccurate or poorly chosen input data can cause convergence issues. Usually, it is bad geometry that is the culprit. You can also try to play with density mixing parameters. 3. Increase the number of k-points: Increasing the number of k-points can improve the convergence of the calculation. This can be done by using a denser k-point mesh or by using a higher-order k-point sampling method. 4. Increase the number of electrons: Increasing the number of electrons in the simulation can improve the convergence of the calculation. This can be done by increasing the simulation cell size or by adding more atoms to the simulation cell.

[@sivakumarneelagandan9004]

I am getting an error as Commands: "mpiexec.exe - n 4 pw.exe.please help

[@PhysWhiz]

You should check the CRASH or the output file under the Results section to get more details on the error.

[@nadamellouk4036]

نبحث عن ترجمة عربي

[@venenatis130]

I'm trying to find the lattice constant before and after a vc-relax. Does anyone know where I could find that information through BURAI?

[@ManasSharma07]

Yeah of course. After running the vc-relax job, just click on the OPT.movie file in the results. This will show you the cell configuration at each iteration. Go to the last iteration by filling in the iteration no. Atomic configuration section, and hit enter. Alternatively, you could just let the movie play through all the iterations. When the movie ends you will see the information about the last iteration. These are your optimized coordinates as well as cell parameters. Just click on 'New Project' to create a new project with these values of atomic coordinates and cell parameters. Thanks for watching my video.

[@venenatis130]

@@ManasSharma07 Thank you for making the videos and responding to my comment! They've been extremely helpful!