wrong band structure using pyprocar #169
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Hey ubaidjmi, I need more information to solve this issue. What code are you using and do you have the inputs? I would guess this is quantum espresso. Logan Lang |
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I am using vasp code, which is giving a band gap of 0.98 eV using post
processing tool Vaspkit, sumo and pymatgen. What inputs do you want?
Mohammad Ubaid, Phd (Physics)
I-PDF, Department of Physics, IIT Kanpur, India
…On Thu, 14 Nov, 2024, 7:29 pm Logan Lang, ***@***.***> wrote:
Hey ubaidjmi <https://github.com/ubaidjmi>,
I need more information to solve this issue. What code are you using and
do you have the inputs?
I would guess this is quantum espresso.
Logan Lang
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Do you have the INCAR, KPOINTS, and POSCAR? |
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Yes, I have!
Please find the attached file.
…On Thu, Nov 14, 2024 at 7:38 PM Logan Lang ***@***.***> wrote:
Do you have the INCAR, KPOINTS, and POSCAR?
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Mohammad Ubaid, Ph.D. (Physics)
Postdoctoral Fellow
Department of Physics
Indian Institute of Technology Kanpur
Kanpur, UP 208016, India
Mob: +91-8800365777
#Electronic
ICHARG = 11
ISMEAR=0
SIGMA=0.05
PREC = Accurate
EDIFF = 1.0E-5
LASPH = .TRUE.
LREAL = .FALSE. # projection done in reciprocal space
ENCUT = 520.00
NELMIN=10
##Geometry
#NSW = 100
#EDIFFG = -0.001
#IBRION = 2
#ISIF = 2
#PBEsol functional
GGA = PS
##Output
LWAVE = .TRUE.
LCHARG = .TRUE.
#LVHAR = .FALSE.
##
##Dos
LORBIT = 10
NEDOS = 2000
EMIN = -30
EMAX = 15
#
##Parallelisation
##LPLANE=.TRUE.
NSIM = 4
NPAR = 4
KPAR = 4
#
LNONCOLLINEAR = .TRUE.
MAGMOM = 72*1
LSORBIT = .TRUE.
VOSKOWN = 1
LMAXMIX = 6
###############POSCAR
Ba4 La4 Cu4 Se12
1.00000000000000
4.2411620410669597 0.0000000000000000 0.0000000000000000
0.0000000000000000 11.1266242302326894 0.0000000000000000
0.0000000000000000 0.0000000000000000 13.7650752175291995
Ba La Cu Se
4 4 4 12
Direct
0.7500000000000000 0.2195220080601175 0.4952739029171696
0.7500000000000000 0.7195220080601175 0.0047260970828376
0.2500000000000000 0.7804779919398825 0.5047260970828376
0.2500000000000000 0.2804779919398825 0.9952739029171624
0.7500000000000000 0.4864516101372303 0.7357320470869979
0.7500000000000000 0.9864516101372303 0.7642679529130021
0.2500000000000000 0.5135483898627697 0.2642679529130021
0.2500000000000000 0.0135483898627697 0.2357320470869979
0.7500000000000000 0.2626475350717072 0.2184534807407204
0.7500000000000000 0.7626475350717072 0.2815465192592796
0.2500000000000000 0.7373524649282928 0.7815465192592796
0.2500000000000000 0.2373524649282928 0.7184534807407204
0.7500000000000000 0.4467124537907026 0.1204978348706902
0.7500000000000000 0.9467124537907026 0.3795021651293098
0.2500000000000000 0.5532875462092974 0.8795021651293098
0.2500000000000000 0.0532875462092974 0.6204978348706902
0.7500000000000000 0.2425486305001883 0.8183108553209095
0.7500000000000000 0.7425486305002025 0.6816891446790905
0.2500000000000000 0.7574513694997975 0.1816891446790905
0.2500000000000000 0.2574513694998117 0.3183108553209095
0.7500000000000000 0.0965260701154094 0.1022573244366285
0.7500000000000000 0.5965260701154094 0.3977426755633715
0.2500000000000000 0.9034739298845906 0.8977426755633715
0.2500000000000000 0.4034739298845906 0.6022573244366285
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
0.00000000E+00 0.00000000E+00 0.00000000E+00
##########KPOINTS
ORC (orthorhombic) G-X-S-Y-G-Z-U-R-T-Z Y-T U-X S-R
16 ! 16 grids
Line-mode
reciprocal
0.000 0.000 0.000 ! \Gamma
0.500 0.000 0.000 ! X
0.500 0.000 0.000 ! X
0.500 0.500 0.000 ! S
0.500 0.500 0.000 ! S
0.000 0.500 0.000 ! Y
0.000 0.500 0.000 ! Y
0.000 0.000 0.000 ! \Gamma
0.000 0.000 0.000 ! \Gamma
0.000 0.000 0.500 ! Z
0.000 0.000 0.500 ! Z
0.500 0.000 0.500 ! U
0.500 0.000 0.500 ! U
0.500 0.500 0.500 ! R
0.500 0.500 0.500 ! R
0.000 0.500 0.500 ! T
0.000 0.500 0.500 ! T
0.000 0.000 0.500 ! Z
0.000 0.500 0.000 ! Y
0.000 0.500 0.500 ! T
0.500 0.000 0.500 ! U
0.500 0.000 0.000 ! X
0.500 0.500 0.000 ! S
0.500 0.500 0.500 ! R
#########Pyprocar
import pyprocar
import matplotlib.pyplot as plt
from matplotlib.ticker import MultipleLocator
dirname = '/home/hp/Optoelctronics_Project/PV_Project/SrCuDyTe3_HSE+SOC/SOC_Projected-band/bands/'
pyprocar.bandsplot(
mode='plain',
width = 4,
elimit=[-2,2],
code='vasp',
dirname=dirname,
fermi=4.7,
)
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Thanks, I am running a spin-polarized calculation without spin-orbit right now. Hopefully, it won't take too long to converge. Then I will try to see what the issue is. I will keep you updated. Logan Lang |
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Ok, thanks for the update.
Mohammad Ubaid, Phd (Physics)
I-PDF, Department of Physics, IIT Kanpur, India
…On Thu, 14 Nov, 2024, 8:27 pm Logan Lang, ***@***.***> wrote:
Thanks,
I am running a spin-polarized calculation without spin-orbit right now.
Hopefully, it won't take too long to converge. Then I will try to see what
the issue is. I will keep you updated.
Logan Lang
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Hey, I calculated the band structure for your system with spin-orbit included and it came out correct. What version of pyprocar are you using?
|
|
Dear Sir,
Thanks for the update.
I am getting band structure using the pyprocar successfully, which I sent
earlier, but it is showing an error attached. Is there any issue with my
installation? That's why it is giving the wrong band bandgap, but the
shapes of the bands are the same.
…On Sun, Nov 17, 2024 at 4:44 AM Logan Lang ***@***.***> wrote:
Hey,
I calculated the band structure for your system with spin-orbit included
and it came out correct. What version of pyprocar are you using?
image.png (view on web)
<https://github.com/user-attachments/assets/17eb60d2-5903-4dc1-ac2a-57ece33d9616>
If you are wondering why the fermi level is different as compared to the
pymatgen, that is because I use the self-consistent fermi energy. I believe
pymatgen parses its plots from the vasprun.xml, but this is parsed from the
band structure directory which will not have the same fermi energy as the
self-consistent fermi energy. I also use a 11 11 11 mesh grid to calculate
the fermi energy.
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Mohammad Ubaid, Ph.D. (Physics)
Postdoctoral Fellow
Department of Physics
Indian Institute of Technology Kanpur
Kanpur, UP 208016, India
Mob: +91-8800365777
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Please provide info about your installation. Python version, pyprocar version, did you check the the version used in python is the one you are assuming? What line did you use to generate the image? (value of fermi?)… keep in mind that we can not reproduce your error without proper documentation.
…______________________________________::::__________________________________________
Prof. Aldo Humberto Romero
Director Research Computing, West Virginia University
Eberly Family Distinguished Professor
Fellow American Physical Society
Editor Physica B, Assistant Editor EPJB, Editor Frontiers in Physics
Section Editor Papers in Physics
Member of the Editorial Board of “Materials” and “Symmetry Physics”
https://scholar.google.com/citations?user=pwte-hQAAAAJ&hl=en
Physics and Astronomy Department
West Virginia University
135 Willey Street, PO Box 6315
111 White Hall
Morgantown, WV 26506
Phone: 304-293-6317
Fax: 304-293-5732
email: ***@***.***
From: ubaidjmi ***@***.***>
Date: Thursday, November 21, 2024 at 3:20 AM
To: romerogroup/pyprocar ***@***.***>
Cc: Subscribed ***@***.***>
Subject: Re: [romerogroup/pyprocar] wrong band structure using pyprocar (Issue #169)
Dear Sir,
Thanks for the update.
I am getting band structure using the pyprocar successfully, which I sent
earlier, but it is showing an error attached. Is there any issue with my
installation? That's why it is giving the wrong band bandgap, but the
shapes of the bands are the same.
On Sun, Nov 17, 2024 at 4:44 AM Logan Lang ***@***.***> wrote:
Hey,
I calculated the band structure for your system with spin-orbit included
and it came out correct. What version of pyprocar are you using?
image.png (view on web)
<https://github.com/user-attachments/assets/17eb60d2-5903-4dc1-ac2a-57ece33d9616>
If you are wondering why the fermi level is different as compared to the
pymatgen, that is because I use the self-consistent fermi energy. I believe
pymatgen parses its plots from the vasprun.xml, but this is parsed from the
band structure directory which will not have the same fermi energy as the
self-consistent fermi energy. I also use a 11 11 11 mesh grid to calculate
the fermi energy.
—
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<#169 (comment)>,
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Mohammad Ubaid, Ph.D. (Physics)
Postdoctoral Fellow
Department of Physics
Indian Institute of Technology Kanpur
Kanpur, UP 208016, India
Mob: +91-8800365777
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Python version Python 3.11.7
Pyprocar version 6.2.1
I am using the following lines:
*import pyprocardirname =
'/home/hp/Optoelctronics_Project/PV_Project/SrCuDyTe3_HSE+SOC/SOC_Projected-band/bands/'pyprocar.bandsplot(
mode='plain', width = 4, elimit=[-2,2], code='vasp',
dirname=dirname, fermi=4.7)*
On Thu, Nov 21, 2024 at 4:53 PM Aldo Romero ***@***.***>
wrote:
… Please provide info about your installation. Python version, pyprocar
version, did you check the the version used in python is the one you are
assuming? What line did you use to generate the image? (value of fermi?)…
keep in mind that we can not reproduce your error without proper
documentation.
______________________________________::::__________________________________________
Prof. Aldo Humberto Romero
Director Research Computing, West Virginia University
Eberly Family Distinguished Professor
Fellow American Physical Society
Editor Physica B, Assistant Editor EPJB, Editor Frontiers in Physics
Section Editor Papers in Physics
Member of the Editorial Board of “Materials” and “Symmetry Physics”
https://scholar.google.com/citations?user=pwte-hQAAAAJ&hl=en
Physics and Astronomy Department
West Virginia University
135 Willey Street, PO Box 6315
111 White Hall
Morgantown, WV 26506
Phone: 304-293-6317
Fax: 304-293-5732
email: ***@***.***
From: ubaidjmi ***@***.***>
Date: Thursday, November 21, 2024 at 3:20 AM
To: romerogroup/pyprocar ***@***.***>
Cc: Subscribed ***@***.***>
Subject: Re: [romerogroup/pyprocar] wrong band structure using pyprocar
(Issue #169)
Dear Sir,
Thanks for the update.
I am getting band structure using the pyprocar successfully, which I sent
earlier, but it is showing an error attached. Is there any issue with my
installation? That's why it is giving the wrong band bandgap, but the
shapes of the bands are the same.
On Sun, Nov 17, 2024 at 4:44 AM Logan Lang ***@***.***> wrote:
> Hey,
>
> I calculated the band structure for your system with spin-orbit included
> and it came out correct. What version of pyprocar are you using?
>
> image.png (view on web)
> <
https://github.com/user-attachments/assets/17eb60d2-5903-4dc1-ac2a-57ece33d9616>
>
> If you are wondering why the fermi level is different as compared to the
> pymatgen, that is because I use the self-consistent fermi energy. I
believe
> pymatgen parses its plots from the vasprun.xml, but this is parsed from
the
> band structure directory which will not have the same fermi energy as
the
> self-consistent fermi energy. I also use a 11 11 11 mesh grid to
calculate
> the fermi energy.
>
> —
> Reply to this email directly, view it on GitHub
> <
#169 (comment)>,
> or unsubscribe
> <
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> .
> You are receiving this because you authored the thread.Message ID:
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Mohammad Ubaid, Ph.D. (Physics)
Postdoctoral Fellow
Department of Physics
Indian Institute of Technology Kanpur
Kanpur, UP 208016, India
Mob: +91-8800365777
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Postdoctoral Fellow
Department of Physics
Indian Institute of Technology Kanpur
Kanpur, UP 208016, India
Mob: +91-8800365777
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Another observation I noticed here is that the k-point distances are different from the original plot you showed. This is because by default PyProcar uses reduced coordinates. To use Cartesian coordinates, set |
|
Thanks. Now, I am getting the correct band structure.
I have one more question:
Can I plot the band structure up to Z point (G-X-S-Y-G-Z-U-R-T-Z) instead
of the full k path?
Actually, I have done band structure calculations along the full k path and
plotted the band structure along the restricted k path using pymatgen. Can
I do this using pyprocar? For your reference, two figures are attached.
…On Thu, Nov 21, 2024 at 10:27 PM Uthpala Herath ***@***.***> wrote:
Another observation I noticed here is that the k-point distances are
different from the original plot you showed. This is because by default
PyProcar uses reduced coordinates. To use Cartesian coordinate, set
kdirect=False.
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Postdoctoral Fellow
Department of Physics
Indian Institute of Technology Kanpur
Kanpur, UP 208016, India
Mob: +91-8800365777
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Dear developers,
I am plotting a bandtsructure of BaCuLaSe3. The band gap is 0.98 eV. Using the pymatgen and sumo plotting tools, I am getting the same plot and showing the same value of the band gap. While using pyprocar, the band gap is 0.37 eV. I am attaching the band structures plotted using all three tools. Please look into the matter and let me know the solution.https://pubs.acs.org/doi/pdf/10.1021/acs.chemrev.0c00026?download=true
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