Hi, I followed all the steps exactly for my system and its working fine. One question, at 18:52 I can three colors: green, red, yellow and then there are region with continuum combination of these colors. What does this continuum represent? Or how to get the color bar and what will be the units and meaning of the numbers represented by that color bar. I thought so far that these are isosurfaces but I think I was wrong. Thanks.
These are just isosurfaces with ppsitive values being of one color and negative of another color. The green red colors you see are artefacts due to the sudden termination of the surface. I don't know why Vesta does that, but they occur only at the ends of unit cell.
@@PhysWhiz @@PhysWhiz Yes exactly. They are occurring at the end of unit cell in my system too. So you means to say there are multiple positive values and all of them are represented by one color and there are multiple negative values which are represented by second color? Then is there any way to get the color bar for such cases in any orbital visualization program?
I don't think the different colors mean anything. The only thing is one color is for positive, the other for negative. The other colors seem to be the artefacts at the boundaries due to sudden termination of the isosurface.
Thank you for all your helpful videos. Could you make a video explaining how to perform by Burai molecule-surface input and how to calculate adsorption energy. PS. I am new in computational solid. Thank you again for your efforts
Hi, All of your tutorials on QE are excellent and I have learned a lot from them. I just have a question on surface passivation by pseuodohydrogen. In many cases, it is common to passivate the surface with pseudohydrogens "with a valency of 0.75". How can I do that in QE. Thanks in advance
Hi, may I ask you a question? Since the scf input file of benzene showing in this video has the output of pi-4 bound lumo, could you show or tell us how to make the scf or pp input file for pi-5 bound lumo? Thank you!
Hello. Thank you for this helpful video. But how can we plot the partial density of a bulk structure at specific energies like for example at energies where there are strong hybridization?
I was following all your steps for Graphene and other systems. My calculation is completing without any errors but I am getting " .dat " file only in output. no ".cub" file which I can give as input to VESTA. I will really appreciate your help in this regards. Thank you.
thank you for your helpful. Can you help me use loop for quantumespresso in command prompt. I had some problems with cygwin. I dont know use loop in command prompt. And i want to use MPICH for the loop. Thank you so much.
Hello, I have seen your paper in PRB, I saw that you applied U potential to Zn 3d 10, in my case I applied U to Sn in SnS2 to correct the band gap which is reported to change from 1.3 eV to 2.0 eV by applying a U of 8 ~ 9 eV, but unfortunately I got no change in the band gap. (I added the U to the Sn and compiled the code because Sn was not added by default). Does anyone know why I got no change in the band gap ? Thanks here is the input file: &control calculation = 'scf' restart_mode='from_scratch' prefix = 'uc_scf_wVCall_U9' outdir = '/home/houcine/outdir' pseudo_dir = '/home/houcine/pseudo' verbosity = 'high' / &system ibrav = 0, nat = 3, ntyp = 2, ecutwfc=50 ecutrho=400 nbnd=26 occupations='smearing',smearing='marzari-vanderbilt',degauss=0.01 lda_plus_u=.true. Hubbard_U(1)=9.0, / &electrons conv_thr=1e-8 / ATOMIC_SPECIES Sn 118.71000 Sn.pbe-dn-rrkjus_psl.1.0.0.UPF S 32.06600 S.pbe-n-kjpaw_psl.1.0.0.UPF ATOMIC_POSITIONS (angstrom) Sn -0.000000000 -0.000000000 -0.000000000 S 0.000000000 2.138507167 1.490115509 S 1.852001313 1.069253463 5.005016561 CELL_PARAMETERS (angstrom) 3.704002867 -0.000000000 0.000000000 -1.852001434 3.207760579 0.000000000 0.000000000 0.000000000 6.495132070 K_POINTS (automatic) 20 20 20 0 0 0 output with U = 9 eV: the Fermi energy is 4.8203 ev ! total energy = -295.68323030 Ry Harris-Foulkes estimate = -295.68323030 Ry estimated scf accuracy < 4.7E-09 Ry The total energy is the sum of the following terms: one-electron contribution = -110.57341350 Ry hartree contribution = 69.58875977 Ry xc contribution = -58.34801420 Ry ewald contribution = -104.08819133 Ry Hubbard energy = 0.00415442 Ry one-center paw contrib. = -92.26793677 Ry -> PAW hartree energy AE = 0.00000000 Ry -> PAW hartree energy PS = 0.00000000 Ry -> PAW xc energy AE = 0.00000000 Ry -> PAW xc energy PS = 0.00000000 Ry -> total E_H with PAW = 69.58875977 Ry -> total E_XC with PAW = -58.34801420 Ry smearing contrib. (-TS) = 0.00141131 Ry convergence has been achieved in 7 iterations output without U: the Fermi energy is 4.8220 ev ! total energy = -295.68741273 Ry Harris-Foulkes estimate = -295.68741273 Ry estimated scf accuracy < 4.6E-09 Ry The total energy is the sum of the following terms: one-electron contribution = -110.56809605 Ry hartree contribution = 69.58176820 Ry xc contribution = -58.34640971 Ry ewald contribution = -104.08819133 Ry one-center paw contrib. = -92.26789442 Ry -> PAW hartree energy AE = 21.91948042 Ry -> PAW hartree energy PS = -21.80773076 Ry -> PAW xc energy AE = -100.63955818 Ry -> PAW xc energy PS = 8.25991411 Ry -> total E_H with PAW = 69.69351786 Ry -> total E_XC with PAW = -150.72605378 Ry smearing contrib. (-TS) = 0.00141056 Ry convergence has been achieved in 7 iterations
The output you show, doesn't show the band gap. I hope you checked it correctly. Also, the value of U is different for different softwares. So it would be better to only compare U values within the same software. Even for ZnS Vasp gives different results than QE. Let me know how you checked the band gap and also which software was used in the literature that you're comparing to.
@@PhysWhiz Thanks for your prompt reply, The literature was using VASP, I checked the band gap by plotting the DOS in both cases with and without U, it is showing the same, no even 1 meV change. I checked many values of U but no change
You might also want to make sure that you're applying the U correction to the correct orbitals. Although I guess, you might be facing a situation similar to mine(ZnS) where the d orbitals were not very delocalised and the Hubbard correction only shifted the d band position, therefore I had to apply the correction to S orbitals. I suggest, you compare the DOS to the experimental DOS and apply the correction so as to get the correct electronic structure.
Sir, I really find your all videos very informative and thanks for uploading this one too. It's of great use for me as I really wanted to know how to do HOMO LUMO plots using quantum espresso. But sir, I also want to know from you how to do electronic charge density (3D) calculations using quantum espresso and plot it (including isosurface plot) with xcrysden visualisation software. I would be really obliged to you then. Thanking you.
Thank you for all your helpful videos. Could you make a tutorial explaining How to know s-, p- and d-orbital contributions (QUANTITATIVELY) in band structure within QUANTUM ESPRESSO package? I mean, similar information as it is found in the following papers: 1. Electronic structures of lead iodide based low-dimensional crystals, PHYSICAL REVIEW B67, 155405 (2003). 2. Small Photocarrier Effective Masses Featuring Ambipolar Transport in Methylammonium Lead Iodide Perovskite: A Density Functional Analysis, J.Phys.Chem.Lett. 2013, 4, 4213−4216.
Hi there! That's a very good question, that even I had when I started surveying DFT literature. Now I don't what software you use for DFT simulations, but if you use Quantum ESPRESSO, then there is utility in there that calculates the projected density of states from the total density of states. The projected density of states tells you what orbital of which atom contributed energy states. For example, here is my paperL link.aps.org/doi/10.1103/PhysRevB.100.045151 where I calculated the projected density of states using QE, to figure out which bands in the band structure correspond to which orbitals of which species. So if you compare the projected(also called partial) density of states, with the band structure, you can say that the bands lying in this energy range are due to this species. Hope I was able to explain it well.
Thank you for this helpful reply. Actually, I used projwfc.x and sumpdos.x. I found the total DOS and DOS of the individual orbitals of each species. when I plot these data (not by using plotproj.x) I was able to find qualitative interpretation. But I couldn't be able to calculate the percentage contribution of each orbital to the total DOS (or to a required band such as VBM or CBM) in some energy range. Can you explain how to get QUANTITATIVE information about which bands in the band structure correspond to which orbitals of which species (similar info is found in 2nd page of the 2nd paper I mentioned above), using QE? Is plotproj.x important for such calculation? I'm not able to understand what the following contents in the input file are (though I read plotproj.f90): threshold ncri first_atomic_wfc, last_atomic_wfc Do you have some explanation about this? Sorry for writing such a lot? With Regards
Thank You so much for these interesting videos and discussion I want to calculate the contribution of each orbital of each species to the valence band maximum (VBM) or to the CBM. To apply the above approach (using partial or projected DOS), how can I find the range of energy for the VBM or to the CBM? I'm using QE. If you like to recommend me any literature my email is lijyetsehay@gmail.com I look forward for your reply
Thank you sir for informative videos, will you please make video on how to do spin polarised calculations using quantum Espresso . and how to perform ph.x calculations for the phase transition with pressure
Hi, I followed all the steps exactly for my system and its working fine. One question, at 18:52 I can three colors: green, red, yellow and then there are region with continuum combination of these colors. What does this continuum represent? Or how to get the color bar and what will be the units and meaning of the numbers represented by that color bar. I thought so far that these are isosurfaces but I think I was wrong. Thanks.
These are just isosurfaces with ppsitive values being of one color and negative of another color. The green red colors you see are artefacts due to the sudden termination of the surface. I don't know why Vesta does that, but they occur only at the ends of unit cell.
@@PhysWhiz @@PhysWhiz Yes exactly. They are occurring at the end of unit cell in my system too. So you means to say there are multiple positive values and all of them are represented by one color and there are multiple negative values which are represented by second color? Then is there any way to get the color bar for such cases in any orbital visualization program?
I don't think the different colors mean anything. The only thing is one color is for positive, the other for negative. The other colors seem to be the artefacts at the boundaries due to sudden termination of the isosurface.
Could u pls make a video on how to get charge density difference for a heterostructure?
Thank you for all your helpful videos. Could you make a video explaining how to perform by Burai molecule-surface input and how to calculate adsorption energy. PS. I am new in computational solid.
Thank you again for your efforts
Hi,
It's actually on my list of things to do. Will try to make it as soon as I can. I'm glad you find these useful.
Hi,
All of your tutorials on QE are excellent and I have learned a lot from them. I just have a question on surface passivation by pseuodohydrogen. In many cases, it is common to passivate the surface with pseudohydrogens "with a valency of 0.75". How can I do that in QE. Thanks in advance
Hi, may I ask you a question? Since the scf input file of benzene showing in this video has the output of pi-4 bound lumo, could you show or tell us how to make the scf or pp input file for pi-5 bound lumo?
Thank you!
Hello. Thank you for this helpful video. But how can we plot the partial density of a bulk structure at specific energies like for example at energies where there are strong hybridization?
I was following all your steps for Graphene and other systems. My calculation is completing without any errors but I am getting " .dat " file only in output. no ".cub" file which I can give as input to VESTA.
I will really appreciate your help in this regards. Thank you.
What if the system has, say, 2 unpaired electrons, that is, is in a triplet state? How do I request that in QE?
Do nspin=2
And set tot_magbetization accordingly.
For example for 2 unpaired electrons tot_magnetization would be 2.
@@PhysWhiz Thanks a lot
thank you for your helpful. Can you help me use loop for quantumespresso in command prompt. I had some problems with cygwin. I dont know use loop in command prompt. And i want to use MPICH for the loop. Thank you so much.
Hi, please, can you make a video about how to install XCrySDen software in windows ?
Hello, I have seen your paper in PRB, I saw that you applied U potential to Zn 3d 10, in my case I applied U to Sn in SnS2 to correct the band gap which is reported to change from 1.3 eV to 2.0 eV by applying a U of 8 ~ 9 eV, but unfortunately I got no change in the band gap. (I added the U to the Sn and compiled the code because Sn was not added by default). Does anyone know why I got no change in the band gap ?
Thanks
here is the input file:
&control
calculation = 'scf'
restart_mode='from_scratch'
prefix = 'uc_scf_wVCall_U9'
outdir = '/home/houcine/outdir'
pseudo_dir = '/home/houcine/pseudo'
verbosity = 'high'
/
&system
ibrav = 0,
nat = 3,
ntyp = 2,
ecutwfc=50
ecutrho=400
nbnd=26
occupations='smearing',smearing='marzari-vanderbilt',degauss=0.01
lda_plus_u=.true.
Hubbard_U(1)=9.0,
/
&electrons
conv_thr=1e-8
/
ATOMIC_SPECIES
Sn 118.71000 Sn.pbe-dn-rrkjus_psl.1.0.0.UPF
S 32.06600 S.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (angstrom)
Sn -0.000000000 -0.000000000 -0.000000000
S 0.000000000 2.138507167 1.490115509
S 1.852001313 1.069253463 5.005016561
CELL_PARAMETERS (angstrom)
3.704002867 -0.000000000 0.000000000
-1.852001434 3.207760579 0.000000000
0.000000000 0.000000000 6.495132070
K_POINTS (automatic)
20 20 20 0 0 0
output with U = 9 eV:
the Fermi energy is 4.8203 ev
! total energy = -295.68323030 Ry
Harris-Foulkes estimate = -295.68323030 Ry
estimated scf accuracy < 4.7E-09 Ry
The total energy is the sum of the following terms:
one-electron contribution = -110.57341350 Ry
hartree contribution = 69.58875977 Ry
xc contribution = -58.34801420 Ry
ewald contribution = -104.08819133 Ry
Hubbard energy = 0.00415442 Ry
one-center paw contrib. = -92.26793677 Ry
-> PAW hartree energy AE = 0.00000000 Ry
-> PAW hartree energy PS = 0.00000000 Ry
-> PAW xc energy AE = 0.00000000 Ry
-> PAW xc energy PS = 0.00000000 Ry
-> total E_H with PAW = 69.58875977 Ry
-> total E_XC with PAW = -58.34801420 Ry
smearing contrib. (-TS) = 0.00141131 Ry
convergence has been achieved in 7 iterations
output without U:
the Fermi energy is 4.8220 ev
! total energy = -295.68741273 Ry
Harris-Foulkes estimate = -295.68741273 Ry
estimated scf accuracy < 4.6E-09 Ry
The total energy is the sum of the following terms:
one-electron contribution = -110.56809605 Ry
hartree contribution = 69.58176820 Ry
xc contribution = -58.34640971 Ry
ewald contribution = -104.08819133 Ry
one-center paw contrib. = -92.26789442 Ry
-> PAW hartree energy AE = 21.91948042 Ry
-> PAW hartree energy PS = -21.80773076 Ry
-> PAW xc energy AE = -100.63955818 Ry
-> PAW xc energy PS = 8.25991411 Ry
-> total E_H with PAW = 69.69351786 Ry
-> total E_XC with PAW = -150.72605378 Ry
smearing contrib. (-TS) = 0.00141056 Ry
convergence has been achieved in 7 iterations
The output you show, doesn't show the band gap. I hope you checked it correctly. Also, the value of U is different for different softwares. So it would be better to only compare U values within the same software. Even for ZnS Vasp gives different results than QE.
Let me know how you checked the band gap and also which software was used in the literature that you're comparing to.
@@PhysWhiz Thanks for your prompt reply, The literature was using VASP, I checked the band gap by plotting the DOS in both cases with and without U, it is showing the same, no even 1 meV change. I checked many values of U but no change
You might also want to make sure that you're applying the U correction to the correct orbitals. Although I guess, you might be facing a situation similar to mine(ZnS) where the d orbitals were not very delocalised and the Hubbard correction only shifted the d band position, therefore I had to apply the correction to S orbitals. I suggest, you compare the DOS to the experimental DOS and apply the correction so as to get the correct electronic structure.
@@PhysWhiz "therefore I had to apply the correction to S orbitals" you mean you applied U to the s orbitals of the Zn ?
Ahh my bad, i mistyped. I meant the S atom 3p orbital along with N d orbital.
Sir, I really find your all videos very informative and thanks for uploading this one too. It's of great use for me as I really wanted to know how to do HOMO LUMO plots using quantum espresso. But sir, I also want to know from you how to do electronic charge density (3D) calculations using quantum espresso and plot it (including isosurface plot) with xcrysden visualisation software. I would be really obliged to you then. Thanking you.
Thank you so much.
Thank you for all your helpful videos. Could you make a tutorial explaining How to know s-, p- and d-orbital contributions (QUANTITATIVELY) in band structure within QUANTUM ESPRESSO package?
I mean, similar information as it is found in the following papers:
1. Electronic structures of lead iodide based low-dimensional crystals, PHYSICAL REVIEW B67, 155405 (2003).
2. Small Photocarrier Effective Masses Featuring Ambipolar Transport in Methylammonium Lead Iodide Perovskite: A Density Functional Analysis, J.Phys.Chem.Lett. 2013, 4, 4213−4216.
Hi there! That's a very good question, that even I had when I started surveying DFT literature.
Now I don't what software you use for DFT simulations, but if you use Quantum ESPRESSO, then there is utility in there that calculates the projected density of states from the total density of states. The projected density of states tells you what orbital of which atom contributed energy states. For example, here is my paperL link.aps.org/doi/10.1103/PhysRevB.100.045151
where I calculated the projected density of states using QE, to figure out which bands in the band structure correspond to which orbitals of which species. So if you compare the projected(also called partial) density of states, with the band structure, you can say that the bands lying in this energy range are due to this species.
Hope I was able to explain it well.
Thank you for this helpful reply.
Actually, I used projwfc.x and sumpdos.x. I found the total DOS and DOS of the individual orbitals of each species. when I plot these data (not by using plotproj.x) I was able to find qualitative interpretation.
But I couldn't be able to calculate the percentage contribution of each orbital to the total DOS (or to a required band such as VBM or CBM) in some energy range. Can you explain how to get QUANTITATIVE information about which bands in the band structure correspond to which orbitals of which species (similar info is found in 2nd page of the 2nd paper I mentioned above), using QE?
Is plotproj.x important for such calculation? I'm not able to understand what the following contents in the input file are (though I read plotproj.f90): threshold ncri first_atomic_wfc, last_atomic_wfc
Do you have some explanation about this?
Sorry for writing such a lot?
With Regards
Thank You so much for these interesting videos and discussion
I want to calculate the contribution of each orbital of each species to the valence band maximum (VBM) or to the CBM. To apply the above approach (using partial or projected DOS), how can I find the range of energy for the VBM or to the CBM?
I'm using QE. If you like to recommend me any literature my email is lijyetsehay@gmail.com
I look forward for your reply
Thank you sir for informative videos, will you please make video on how to do spin polarised calculations using quantum Espresso .
and how to perform ph.x calculations for the phase transition with pressure