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Phys Whiz
Индия
Добавлен 12 дек 2015
Tutorials on Physics, Computational Material Science, Scientific Computing, and more
The tutorials and lectures are developed by physicists holding PhD degrees or senior PhD candidates.
Phys Whiz Team:
Dr. Manas Sharma, PhD Physics from University of Jena, Germany
Ms. Priyanshi Bhasin, PhD (Physics) candidate at Indian Institute of Science, Bangalore, India
Follow us on:
Facebook: bragitoff
Website: www.bragitoff.com
The tutorials and lectures are developed by physicists holding PhD degrees or senior PhD candidates.
Phys Whiz Team:
Dr. Manas Sharma, PhD Physics from University of Jena, Germany
Ms. Priyanshi Bhasin, PhD (Physics) candidate at Indian Institute of Science, Bangalore, India
Follow us on:
Facebook: bragitoff
Website: www.bragitoff.com
How to Calculate Cohesive Energy of a Crystal using TURBOMOLE's RIPER module? [TUTORIAL]
In this hands-on TURBOMOLE (Riper) tutorial, I walkthrough the process of calculating the cohesive energy (per atom) of a crystal, using Silicon as an example.
The formula for the cohesive energy (per atom) is
E_\mathrm{coh/atom}=-(E_\text{bulk(per atom)}-E_\text{isolated atom})
The input and output files form the tutorial are available here: www.bragitoff.com/wp-content/uploads/2024/05/Cohesive_Energy_TUTORIAL_Turbomole_RIPER.zip
The CIF file for the Silicon crystal used in this tutorial is available here: www.bragitoff.com/wp-content/uploads/2024/05/Silicon_Conventional_Cell.cif
I used the material mp-149 from materialsproject.org to obtain the CIF file: next-gen.materialsproject.org/materi...
The formula for the cohesive energy (per atom) is
E_\mathrm{coh/atom}=-(E_\text{bulk(per atom)}-E_\text{isolated atom})
The input and output files form the tutorial are available here: www.bragitoff.com/wp-content/uploads/2024/05/Cohesive_Energy_TUTORIAL_Turbomole_RIPER.zip
The CIF file for the Silicon crystal used in this tutorial is available here: www.bragitoff.com/wp-content/uploads/2024/05/Silicon_Conventional_Cell.cif
I used the material mp-149 from materialsproject.org to obtain the CIF file: next-gen.materialsproject.org/materi...
Просмотров: 410
Видео
How to Calculate Adsorption Energy using Quantum ESPRESSO and DFT? [TUTORIAL]
Просмотров 2,6 тыс.4 месяца назад
In this new tutorial, I'll be showing you how to use Quantum Espresso and Density Functional Theory (DFT) to calculate the adsorption energy of a molecule on a surface/slab using the water molecule (H2O) on a lithium hydride (LiH) surface as an example. This is a really important calculation in surface science and catalysis research. We'll be following a paper from 2017 that looked at this same...
How to Calculate Cohesive Energy using Quantum Espresso? [TUTORIAL]
Просмотров 1,4 тыс.4 месяца назад
In this hands-on Quantum ESPRESSO tutorial, I walkthrough the process of calculating the cohesive energy (per atom) of a crystal, using Silicon as an example. The formula for the cohesive energy (per atom) is E_\mathrm{coh/atom}=-(E_\text{bulk(per atom)}-E_\text{isolated atom}) The input and output files form the tutorial are available here: www.bragitoff.com/wp-content/uploads/2024/05/Cohesive...
How to Calculate BSSE-Corrected Adsorption Energy using TURBOMOLE? [TUTORIAL] (Pt. 2)
Просмотров 2484 месяца назад
This is a follow-up to my previous tutorial on the calculation of adsorption energy using TURBOMOLE (link: ruclips.net/video/khUakVfQgyg/видео.html). In this detailed walkthrough, I demonstrate the procedure of calculating the basis set superposition error (BSSE) corrected adsorption energy of a molecule on top of a surface. BSSE causes the adsorbate (molecule) to be artificially stabilized as ...
How to Calculate Adsorption Energy using RIPER module of TURBOMOLE? [TUTORIAL] (Pt. 1)
Просмотров 3884 месяца назад
In this detailed walkthrough, I demonstrate the procedure of calculating the adsorption energy of a molecule on top of a surface. As an example, the adsorption energy of the H2O (water) molecule on top of the LiH (001) surface is calculated. The structures for the calculation are obtained from the supplementary information of this paper: pubs.aip.org/aip/jcp/article/146/20/204108/671673/A-compa...
How to Calculate & Plot Absorption Spectrum using RT-TDDFT? [TURBOMOLE TUTORIAL]
Просмотров 2864 месяца назад
This video is a detailed walkthrough of the process of calculating and plotting the absorption spectrum of a water molecule using the RT-TDDFT (real time-time dependent density functional theory) implementation in the RIPER module of TURBOMOLE. The files used in the tutorial can be found here: www.bragitoff.com/wp-content/uploads/2024/04/H2O.zip RIPER-Tools Web App: ripertools.turbomole.org The...
BAND STRUCTURE of MoS2 (2D) layer using TURBOMOLE (RIPER) [TUTORIAL]
Просмотров 8078 месяцев назад
In this tutorial, I show in detail, the process to calculate and plot the band structure of a 2D material (MoS2), using the RIPER module of the TURBOMOLE electronic structure package. The tutorial shows how to reproduce the band structure of MoS2 found on the C2DB website (cmrdb.fysik.dtu.dk/c2db). I walk through the procedure of obtaining the cell parameters and atomic coordinates from the C2D...
Calculating and Plotting BAND STRUCTURE of SILICON BULK-3D Crystal using TURBOMOLE (RIPER)[TUTORIAL]
Просмотров 6789 месяцев назад
In this tutorial, I show in detail, the process to calculate and plot the band structure of a bulk 3D material with Silicon (Cubic Diamond structure) as example, using the RIPER module of the TURBOMOLE electronic structure package. The tutorial shows how to reproduce the band structure of Si found on the materials project website. To perform a periodic DFT calculation with TURBOMOLE, one needs ...
How to run a Periodic DFT calculation using RIPER module of TURBOMOLE? [TUTORIAL]
Просмотров 5229 месяцев назад
In this tutorial, I show you all how to run a PERIODIC density functional theory (DFT) calculation using the TURBOMOLE's RIPER module in a step-by-step fashion. RIPER module allows to run both molecular and periodic DFT calculations using the resolution of identity (RI) approximation (density fitting) for the Coulomb term. I walk through all the steps, starting from the explanation of some basi...
CrysX-3D Viewer DEMO: Benzene Molecular Orbital on a Plane
Просмотров 32411 месяцев назад
Aesthetic Visualization of the Benzene's Molecular Orbital isosurface using particle shaders with shadows cast on a dark plane. #Shorts
My Talk at DokDok Lite 2021 on Density Functional Embedding Theory for Excited States
Просмотров 329Год назад
This talk was given at DokDok Lite 2021 (www.asp.uni-jena.de/doctoral-phd/former-events/dokdok-lite-2021) on September 3, 2021 I present some of my PhD work in this talk. The work has also been published in Journal of Chemical Theory and Computation. Read it here: pubs.acs.org/doi/10.1021/acs.jctc.2c00380 Abstract: One of the main challenges in the application of accurate wavefunction theory (W...
Electron Dynamics animation of Tetraphenylporphyrin (TPP) and Zn-TPP dimers via TURBOMOLE & CrysX
Просмотров 326Год назад
This is a visualization of the time-dependent differential electron density (excited density - ground state density) of TPP and Zn-TPP dimers under an intense laser pulse of intensity 1.5 TW/cm^2. We notice that there is very little coupling between the monomers thereby one should not expect a significant difference in the absorption or HHG spectra compared to the monomer case. I created this s...
Electron Dynamics of Tetraphenylporphyrin and Zinc-Tetraphenylporphyrin via TURBOMOLE (RT-TDDFT)
Просмотров 355Год назад
This is a visualization of the time-dependent differential electron density (excited density - ground state density) of TPP and Zn-TPP under an intense laser pulse of intensity 1.5 TW/cm^2. I created this scientific animation as a part of the following collaborative research article (open access): Resonance Effect in Brunel Harmonic Generation in Thin Film Organic Semiconductors onlinelibrary.w...
How to perform Molecular Geometry Optimization using RIPER and JOBEX of TURBOMOLE? [TUTORIAL]
Просмотров 895Год назад
In this tutorial, I walk you through the procedure of optimizing the geometry of a molecule using the RIPER module and JOBEX script of TURBOMOLE. Here are the files used in the tutorial: www.bragitoff.com/wp-content/uploads/2023/05/benzene_geom_opt_riper.zip TURBOMOLE Documentation: www.turbomole.org/turbomole/turbomole-documentation/ TURBOMOLE Tutorials Playlist: ruclips.net/p/PLUhYFZgYOn8eyto...
How to run a Molecular DFT calculation using RIPER module of TURBOMOLE? [TUTORIAL]
Просмотров 1,5 тыс.Год назад
How to run a Molecular DFT calculation using RIPER module of TURBOMOLE? [TUTORIAL]
How to visualize Crystal structure from .CIF in Jmol? [TUTORIAL] #PrimitiveCell #SuperCell
Просмотров 2,1 тыс.Год назад
How to visualize Crystal structure from .CIF in Jmol? [TUTORIAL] #PrimitiveCell #SuperCell
My Talk at ETSF 2022 on Density Functional Embedding Theory for Excited States
Просмотров 717Год назад
My Talk at ETSF 2022 on Density Functional Embedding Theory for Excited States
My Award Winning Talk at EMRS 2021 (Fall) on Density Functional Embedding Scheme
Просмотров 904Год назад
My Award Winning Talk at EMRS 2021 (Fall) on Density Functional Embedding Scheme
Electron Dynamics of Resonant Excitation of Water molecule using RT-TDDFT (Animation)
Просмотров 1,7 тыс.2 года назад
Electron Dynamics of Resonant Excitation of Water molecule using RT-TDDFT (Animation)
MOLECULAR ORBITALS and DENSITY Plotting using RIPER (TURBOMOLE) - [TUTORIAL]
Просмотров 1,8 тыс.2 года назад
MOLECULAR ORBITALS and DENSITY Plotting using RIPER (TURBOMOLE) - [TUTORIAL]
How to convert a basis set from one format to another? [TUTORIAL]
Просмотров 6842 года назад
How to convert a basis set from one format to another? [TUTORIAL]
PROBABILITY of RANDOM walkers MEETING on a 2D grid - [EXPLAINED]
Просмотров 3613 года назад
PROBABILITY of RANDOM walkers MEETING on a 2D grid - [EXPLAINED]
VISUALIZING FOURIER Series in ACTION | PYTHON Simulation / ANIMATION
Просмотров 4,6 тыс.3 года назад
VISUALIZING FOURIER Series in ACTION | PYTHON Simulation / ANIMATION
PERIODIC function in PYTHON | ANIMATED VISUALIZATION
Просмотров 1,9 тыс.3 года назад
PERIODIC function in PYTHON | ANIMATED VISUALIZATION
Estimating PI | Monte Carlo Animation | PYTHON Simulation
Просмотров 2,8 тыс.3 года назад
Estimating PI | Monte Carlo Animation | PYTHON Simulation
ANIMATION - BISECTION METHOD | Python Simulation in Action
Просмотров 2 тыс.3 года назад
ANIMATION - BISECTION METHOD | Python Simulation in Action
BISECTION Method for ROOT FINDING - Explained with an Example
Просмотров 6 тыс.3 года назад
BISECTION Method for ROOT FINDING - Explained with an Example
How to get a PhD in Germany/Europe? [INDIAN's Perspective]
Просмотров 8883 года назад
How to get a PhD in Germany/Europe? [INDIAN's Perspective]
Three-Way Duel (Stand-Off) - PROBABILITY Puzzle [SOLUTION]
Просмотров 1,6 тыс.3 года назад
Three-Way Duel (Stand-Off) - PROBABILITY Puzzle [SOLUTION]
SIMULATION - Probability of RANDOM WALKERS meeting on a 4x4 GRID
Просмотров 3863 года назад
SIMULATION - Probability of RANDOM WALKERS meeting on a 4x4 GRID
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I have problem. I hope you help me. My linear plot does not appear after linear fitting :(((
Sir please make a video that how to make SCF input file for BXF3 (S,Al,P) using BURAI
How to create CIF an input file for BSF3 (X=S,Al,P) this compound using BURAI Then how to run
We can notice that the some arrows are pointing to the direction perpendicular to [1,0,0]...
Thanks, saves time on reading docs).
Maybe it would be better to solve (1-x^2)y'' - 2xy' + n(n+1)y = 0 c[0] = 1 - (n&1) c[1] = (n&1) s = c[0]; for(k=0;k < n;k++) { c[k+2] = (double)(k-n)*(k+n+1)/((k+2)(k+1))c[k]; s += c[k+1]; } s = 1.0/s; for(k=0;k<=n;k++) c[k] *=s; This code gives us extra coefficient which should be ignored This code can generate these polynomial in O(n) time
best for upscaths optipnal
I am unable to activate the materials API search option in BURAI
Hi. Nice video. I am trying to do scf calculations for CuBi2O4 but unable to do that I am getting an error
Hello sir, very nice lecture. Can you also make a tutorial on how to calculate attachment energy of a surface using QE? Appreciate your efforts!!
if it's FCC why didnt we use Ibrav 2?
I am trying to calculate cohesive energy of ScAl2. ans coming out is much much larger than actual value. Another thing is that I am trying with nspin=2, nspin=1 for Sc, In both cases energy is coming as almost equal. Where I am going wrong. pls give me suggestions . I am giving my input script below, for ScAl2, Sc, and Al ScAl2 &CONTROL calculation = 'scf' outdir = './out/' prefix = 'ScAl2' pseudo_dir = '.' verbosity = 'high' / &SYSTEM degauss = 1d-02 ecutrho = 400d0 ecutwfc = 40d0 ibrav = 0 nat = 24 ntyp = 2 occupations = 'smearing' smearing = 'gaussian' / &ELECTRONS conv_thr = 1.2000000000d-09 electron_maxstep = 150 mixing_beta = 4.0000000000d-01 startingpot = 'atomic' startingwfc = 'atomic+random' / ATOMIC_SPECIES Sc 44.9559 Sc.pbe-spn-kjpaw_psl.1.0.0.UPF Al 26.9815 Al.pbe-nl-kjpaw_psl.1.0.0.UPF ATOMIC_POSITIONS {crystal} Sc 0.00000000000000 0.00000000000000 0.50000000000000 Sc 0.25000000000000 0.25000000000000 0.75000000000000 Sc 0.00000000000000 0.50000000000000 0.00000000000000 Sc 0.25000000000000 0.75000000000000 0.25000000000000 Sc 0.50000000000000 0.00000000000000 0.00000000000000 Sc 0.75000000000000 0.25000000000000 0.25000000000000 Sc 0.50000000000000 0.50000000000000 0.50000000000000 Sc 0.75000000000000 0.75000000000000 0.75000000000000 Al 0.12500000000000 0.12500000000000 0.12500000000000 Al 0.62500000000000 0.37500000000000 0.87500000000000 Al 0.37500000000000 0.12500000000000 0.37500000000000 Al 0.37500000000000 0.37500000000000 0.12500000000000 Al 0.12500000000000 0.62500000000000 0.62500000000000 Al 0.62500000000000 0.87500000000000 0.37500000000000 Al 0.37500000000000 0.62500000000000 0.87500000000000 Al 0.37500000000000 0.87500000000000 0.62500000000000 Al 0.62500000000000 0.12500000000000 0.62500000000000 Al 0.12500000000000 0.37500000000000 0.37500000000000 Al 0.87500000000000 0.12500000000000 0.87500000000000 Al 0.87500000000000 0.37500000000000 0.62500000000000 Al 0.62500000000000 0.62500000000000 0.12500000000000 Al 0.12500000000000 0.87500000000000 0.87500000000000 Al 0.87500000000000 0.62500000000000 0.37500000000000 Al 0.87500000000000 0.87500000000000 0.12500000000000 K_POINTS {automatic} 8 8 8 0 0 0 CELL_PARAMETERS {angstrom} 7.55530537 0.00000000 0.00000000 0.00000000 7.55530537 0.00000000 0.00000000 0.00000000 7.55530537 Sc &CONTROL calculation = 'scf' outdir = './out/' prefix = 'Sc' pseudo_dir = '.' verbosity = 'high' / &SYSTEM degauss = 1d-02 angle1(1) = 0.00000d+00 angle2(1) = 0.00000d+00 constrained_magnetization = 'atomic' ecutrho = 400d0 ecutwfc = 40d0 ibrav = 0 nat = 1 ntyp = 1 nspin = 2 occupations = 'smearing' smearing = 'gaussian' starting_magnetization(1) = 1.00000d-01 / &ELECTRONS conv_thr = 1.2000000000d-09 electron_maxstep = 150 mixing_beta = 4.0000000000d-01 startingpot = 'atomic' startingwfc = 'atomic+random' / ATOMIC_SPECIES Sc 44.9559 Sc.pbe-spn-kjpaw_psl.1.0.0.UPF ATOMIC_POSITIONS {crystal} Sc 0.50000000000000 0.50000000000000 0.50000000000000 K_POINTS {gamma} CELL_PARAMETERS {angstrom} 14.00000000 0.00000000 0.00000000 0.00000000 14.00000000 0.00000000 0.00000000 0.00000000 14.00000000 Al &CONTROL calculation = 'scf' outdir = './out/' prefix = 'Al' pseudo_dir = '.' verbosity = 'high' / &SYSTEM degauss = 1d-02 angle1(1) = 0.00000e+00 angle2(1) = 0.00000e+00 constrained_magnetization = "atomic" ecutrho = 400d0 ecutwfc = 40d0 ibrav = 0 nat = 1 ntyp = 1 nspin = 2 occupations = 'smearing' smearing = 'gaussian' starting_magnetization(1) = 1.00000e-01 / &ELECTRONS conv_thr = 1.2000000000d-09 electron_maxstep = 150 mixing_beta = 4.0000000000d-01 startingpot = 'atomic' startingwfc = 'atomic+random' / ATOMIC_SPECIES Al 26.9815 Al.pbe-nl-kjpaw_psl.1.0.0.UPF ATOMIC_POSITIONS {crystal} Al 0.87500000000000 0.87500000000000 0.12500000000000 K_POINTS {gamma} CELL_PARAMETERS {angstrom} 14.00 0.00000000 0.00000000 0.00000000 14.00 0.00000000 0.00000000 0.00000000 14.00
The energy of Sc, using your input file is not equal with and without spin polarization. I'm getting a value of -156.63416812 Ry without spoin polarization and -156.64404984 Ry with spin polarization. Ry is a big unit of energy. 1 Ry= 13.6 eV. Please note, I use a higher value of Ecutwfc= and Ecutrho, compared to what you used: ecutrho = 4.42315e+02 ecutwfc = 4.91461e+01 Also, I am getting a cohesive energy of -4.2 eV/atom. What are you getting and what is the expected value?
@@ManasSharma07 what is the formula used for this purpose... pls elaborate. the value 156 I am also getting for Al I am getting 39.2 Ry. and for ScAl2 this is around 1888 ry. what is the formula used?
@@sankhasubhramukhopadhyay5633 You didn't answer my question in my comment: What are you getting and what is the expected value?
@ManasSharma07 I am getting value around 117 Ry. And actual ans is 4.16 eV ..your calculation is right but what formula I have to use
@@sankhasubhramukhopadhyay8005 This is the formula I used www.wolframalpha.com/input?i=-1888.553770%2F24+-+%288*-156.64404984+%2B+16*-39.24939399%29%2F24
Sir I have a small question. when the electronic configuration is like [Ar] 4s² 3d¹ what nspin value I have to take? As 4s is filled and it is the outer shell so nspin = 1. Is this correct?
The 3d electron is also a valence electron. Since there is one unpaired electron the value of nspin should be 2. Also you can always verify these things. You can run two calculations: one with nspin=1 and nspin=2. Then you can compare the energies from the two calculations. The one with the lower energy would be the correct option.
@@PhysWhiz thank you sir
No need to call me "sir".
How to get softwares?
How to simulation of energy storage device.
Bhai tu kaun hai bhai tere education ko toh rehdne do tumhare cvv bio data ka blogpage ko samjhne main alag se coaching institutes kholne chhaiye Show-off elon musk tony stark ke saste version
very nice tutorial. could you make adsorption energies of OH− molecules NiO?
Thank you for the video. Small question. Which parameters should we keep the same calculating entire system and isolated atoms? For instance, if we use smearing for entire system, should we use exact the same degauss for isolated atoms? Or we can choose smaller degauss, if it is applicable, to decrease smearing contribution?
Nice tutorial!!! Can you explain why we use 12 angstroms lattice parameter for isolated atom calculation what will heppen in case if I increase this lattice parameter to 20 angstroms or otherwise decrease it to 7 angstroms ?
I think I already mentioned this in the video. But the key thing is that Quantum ESPRESSO inherently applies periodic boundary conditions to your system in 3 dimensions. This means that whatever system you define it will essentially be repeated with the periodicity given by the lattice parameters. For cohesive energy, you require the energy of an isolated atom. But Quantum ESPRESSO will repeat the atom I have in my system periodically. So if I have a small lattice parameter, then the atom will have periodic images that are nearer. If the lattice parameter is large, then the periodic images would be further. If the images are nearer then they will interact. You wouldn't call an atom interacting with other similar atoms as isolated. So this wouldn't work. If the periodic images are farther, then after a certain threshold, the interactions between them would become negligible. Then you can consider your atom to be isolated. You can find out the threshold or the lattice parameter size after which the interactions become negligible yourself, by running SCF for different lattice parameters. Once the energy stops changing beyond a threshold, you can consider the atom to be effectively isolated.
Recently I have installed burai, but atoms are not visible, can you make a video on this
I have faced this issue in the past as well. I was able to fix it by updating the display drivers but unfortunately I can't give you a definite fix.
Very helpful. Thanks!!!
Hi Is relax calculation need to perform for all three structure?
Yes. Ideally, you would need to optimize the molecule in its ga phase (isolated molecule); optimize (cell+atomic positions) the bulk material and then using those lattice parameters, create a surface and then optimize only the atomic positions of the top few layers. In my case, I was trying to reproduce a result of the paper, so I just followed what they did.
Thanks a lot! the tutorial was really helpful for me
Glad to hear that!
how to put space group in this burai
8 years later you saved my CS C++ exam!
Could u pls make a video on how to get charge density difference for a heterostructure?
u just save my wife's notes en el poli:3 THANK U, I wll give some papas enchilosas if u come to Mexico, amigooooo
What should I do if I cannot select the second atom when measuring the bond length with vesta
Nice ... Is it possible to calculate the charge transfer (i.e., no. of electrons transferred during the physisorption process) and adsorption energy using Burai??
Unfortunately, you can't do it directly with burai. You would need to run a few potprocessing calculations and then also utilize external scripts/software.
Is it possible to calculate the charge transfer (i.e., no. of electrons transferred during physisorption process) and adsorption energy using Burai??
It is not possible through BURAI. But essentially you just need to generate a cube file of your system's density and then process it. This might be useful: ruclips.net/video/FrY8Sj0zUus/видео.htmlsi=Gt1USzv3mA7IyHzv
Very nice video, can we perform these calculations for polymers and gel polymer electrolyte. Please help me
Hi, I'm afraid I'm not familiar with DFT calculations of Polymers. Could you please refer me to a paper so that I can better answer your question?
@@PhysWhiz Sorry Sir, I did not get much information in case of quantum esspresso
Good one. Nice. Could you inform how to find interstitial sites and Bader charge using Quantum Espresso? Any tutorial would be great.
Nice. Could you inform how to find interstitial sites and Bader charge using Quantum Espresso?
Good work
Thank you Thanks a lot. excellent video. Do you have a video about installing the TURBOMOLE program?
Once you buy Turbomole you get all the compiled binaries (executables) that you just have to unpack. So there is not compilation needed and the installation is basically just unpacking, so there's not much to make a tutorial for it.
Very informative sir . Thank you
very useful tutorial. Thank you.
Thank you sir, helpful video 👍
Thanks.
How can I put High symmetry points in burai for TiO2
Good work
Please make a video on magnetic properties calculation using CASTEP.
Very nice. We need to write program for Fourier fit? Is there any suggestions.
Can I run these files in BURAI instead of Quantum espresso?
Thank you so much for clearing concept Sir. One of the best videos on Fourier series, could you please upload questions regarding this.
thanks! you are the only one that explains why which terms don't commute!
is it possible to get wfn/wfx/molden file at each time step (not CUBE file)?
There are some amazing teachers in the world, and you are definitely one of them.
Very useful