Re: [QE-users] Problem with DFPT using SCAN

[Paolo Giannozzi]

On 16/05/2024 21:39, Nupur Mehra wrote:

I'm trying to perform a DFPT calculation using the SCAN functional. I 
tried to do it using the QE version 6.4.1 first but I ran into the issue 
about the phonon code with meta-GGA functionals not being available.


they aren't yet, and I doubt they are going to be available any time soon


I was suggested to use another version of QE (5.1.1) to do this calculation.


bad advice

Paolo
--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
AVAILABLE POSITION: 
https://physicslab.uniud.it/persone/paolo-giannozzi/prin2022

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[QE-users] Problem with DFPT using SCAN

[Nupur Mehra]

Hi all,
I'm trying to perform a DFPT calculation using the SCAN functional. I tried
to do it using the QE version 6.4.1 first but I ran into the issue about
the phonon code with meta-GGA functionals not being available. I was
suggested to use another version of QE (5.1.1) to do this calculation.
I installed QE (5.1.1) with the libxc (3.0.0). When I run a plane wave scf
calculation with SCAN, I get an error saying "SCAN: unrecognized dft". It
seems like there is some issue with linking libxc with QE. For linking
libxc with QE, I updated the make.sys.in in the install directory by doing
DFLAGS+=-D__LIBXC, LD_LIBS+=-L/path_to_libxc_lib/ -lxcf90 -lxc and
IFLAGS+=-I/path_to_libxc_include/ and then configured it. I had also tried
updating LD_LIBS+= /path_to_libxc_lib/libxc.a and then configuring as per a
previous post, but I still got the same error. I have included the
configure log file and make.sys file with the email for more information.

I would really appreciate some help with this issue.

Thank you in advance.

Best regards,

*Nupur Mehra*
PhD Student | Yue Group
Robert Frederick Smith School of Chemical and Biomolecular Engineering
Cornell University


make_sys
Description: Binary data


config.log
Description: Binary data
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Re: [QE-users] users Digest, Vol 202, Issue 12

[Jing Lian Ng]

Hello Omar and Prasenjit,

Thank you for the advice! The calculation proceeds fine now when I turn off
the dftd3_threebody tag. Another question I had in mind is that are there
particular reasons for running D3 with BJ damping or D3M/D3M-BJ instead of
the standard "zero damping" D3?

On Wed, May 15, 2024 at 5:00 AM 
wrote:

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> Today's Topics:
>
>1. Not able to converge Triplet O2 with quantum espresso v   7.2
>   (AKHILESH SHARMA 22909003)
>2. Phonon calculation with DFT-D3 correction (Jing Lian Ng)
>3. Re: Phonon calculation with DFT-D3 correction (Omar Ashour)
>4. Re: Phonon calculation with DFT-D3 correction (Ghosh, Prasenjit)
>5. [SPAM] Inquiry Regarding the libxc (=?ISO-8859-1?B?emhvdWNoYW8=?=)
>6. Re: [SPAM] Inquiry Regarding the libxc (Paolo Giannozzi)
>
>
> --
>
> Message: 1
> Date: Tue, 14 May 2024 15:58:23 +0530
> From: AKHILESH SHARMA 22909003 
> To: users@lists.quantum-espresso.org
> Subject: [QE-users] Not able to converge Triplet O2 with quantum
> espresso v  7.2
> Message-ID:
>  aapas...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello everyone
>
> I'm currently facing challenges in optimizing the triplet state of an
> dioxygen molecule within Quantum espresso version7.2. In order to calculate
> the change in  energy in my reaction pathway, it requires the energy of a
> dioxygen molecule. I've already set up the calculation with the parameters
> specified in the input file but at the end it is not converging. Below,
> I've provided both the input and output files for your reference and I have
> also attached the image of the error. I would greatly appreciate your
> assistance in resolving this issue.
> [image: image (1).png]
> -- next part --
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> --
>
> Message: 2
> Date: Tue, 14 May 2024 16:50:28 -0500
> From: Jing Lian Ng 
> To: users@lists.quantum-espresso.org
> Subject: [QE-users] Phonon calculation with DFT-D3 correction
> Message-ID:
>  xek...@mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hello all,
>
> I am currently trying to perform phonon calculation with DFT-D3 correction.
> Based on what I read from d3hess.x documentation, I believe I can include
> dispersion effects on vibrational frequencies by:
>
>1. Relax / Scf calculation
>2. run d3hess.x
>3. run ph.x
>
> However, I encounter an error on step2, with the error message being:
>
>  %%%
>  task #28
>  from pbcgdisp : error # 1
>  Atom displacement not implemented with the threebody term
>  %%
>
> My input file for scf is as follows:
>
> ##
> /
> 
>ntyp = 1
>nat  = 2
>ibrav= 0
>ecutwfc = 100
>ecutrho = 400
>vdw_corr = 'DFT-D3'
> /
> 
>mixing_mode = 'plain'
>mixing_beta = 0.3
> /
> 
> /
> 
> /
> ATOMIC_SPECIES
> H 1.008 H.upf
>
> CELL_PARAMETERS angstrom
> 5.216575 0.00 0.00
> 0.00 6.049260 0.00
> -6.40884630521040 0.00 36.38325638013446
> ##
>
> Can someone advise 

Re: [QE-users] Error in routine memory_report (1): more bands than PWs!

[Paolo Giannozzi]

You have forgotten to set the correct lattice parameter somewhere: your 
structure is extremely dense


Paolo
On 15/05/2024 12:13, Максим Арсентьев wrote:

Dear users and developers,
After running carbon allotrope relaxation I got this error:
Error in routine memory_report (1): more bands than PWs!
Best regards,
Dr. Maxim Arsentev
Research Fellow of Infochemistry Scientific Center (ISC)
ITMO University

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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine Italy, +39-0432-558216
AVAILABLE POSITION: 
https://physicslab.uniud.it/persone/paolo-giannozzi/prin2022

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[QE-users] Re - K_POINTS problem of band_interpolation.x

[Ivan Carnimeo]

It seems there is something that needs to be fixed to enable reading input with 
k-points labels.

You can provide k-points coordinates instead, as in the example input file:

https://gitlab.com/QEF/q-e/-/blob/develop/PP/examples/exx_interpolated_bands_example/pbe_fourier/fourier.in

IC

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Re: [QE-users] [SPAM] temperature of the output electronic properties in QE

[Md. Jahid Hasan Sagor]

Hi,

Thank you for your response. So, if I use the CIF files cell
structure (@298 K), and run the QE without optimizing the atoms
position/Unit cell, the output of QE will be at that temperature (@298K),
right?. However, if I optimize the cell structure/atom position using
vc-relax.in/relax.in, the output of QE will be at 0 K ?

Thanks!

Best
Md Jahid Hasan
PhD Student
University of Maine

On Thu, May 16, 2024 at 11:42 AM Husak Michal via users <
users@lists.quantum-espresso.org> wrote:

> Data obtained by vc-relax corresponds to 0 K.
> Data obtained by relax with RT cell parameters fixed corresponds
> to not relaxed QM minimum with undefined temperature.
> To describe correctly structure at given temperature you must use quantum
> dynamic calculations ...
>
> Michal Husak
> UCT Prague
> 
> From: users  on behalf of Md.
> Jahid Hasan Sagor 
> Sent: Thursday, May 16, 2024 4:34:41 PM
> To: Quantum ESPRESSO users Forum
> Subject: [SPAM] [QE-users] temperature of the output electronic properties
> in QE
>
> Hi,
>
> What's the temperature of the output electronic properties, even if we use
> 298 K cell info (atom position) as an input?
>  Normally to prepare input file (structure of materials) for QE, I
> searched the corresponding CIF file from this website (
> http://www.crystallography.net/cod/result.php), after that I use Vesta to
> get the relevant atomic positions and lattice parameter. I have a question
> regarding that. Most of the CIF files cell temperature are at 298 K, so if
> we use the structural data from that CIF (298 K) and run QE( after
> performing Optimizing atomic positions (relax.in),
> optimizing Unit cell (vc-relax.in)) to find
> electronic properties (e.g, density of states, fermi level), Are the output
> data of QE represent the temperature of 0 K?
>
> Thanks
>
> Best
> Md Jahid Hasan
> PhD Student
> University of Maine
> ___
> The Quantum ESPRESSO community stands by the Ukrainian
> people and expresses its concerns about the devastating
> effects that the Russian military offensive has on their
> country and on the free and peaceful scientific, cultural,
> and economic cooperation amongst peoples
> ___
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>
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Re: [QE-users] [SPAM] temperature of the output electronic properties in QE

[Husak Michal via users]

Data obtained by vc-relax corresponds to 0 K.
Data obtained by relax with RT cell parameters fixed corresponds
to not relaxed QM minimum with undefined temperature.
To describe correctly structure at given temperature you must use quantum
dynamic calculations ...

Michal Husak
UCT Prague

From: users  on behalf of Md. Jahid 
Hasan Sagor 
Sent: Thursday, May 16, 2024 4:34:41 PM
To: Quantum ESPRESSO users Forum
Subject: [SPAM] [QE-users] temperature of the output electronic properties in QE

Hi,

What's the temperature of the output electronic properties, even if we use 298 
K cell info (atom position) as an input?
 Normally to prepare input file (structure of materials) for QE, I searched the 
corresponding CIF file from this website 
(http://www.crystallography.net/cod/result.php), after that I use Vesta to get 
the relevant atomic positions and lattice parameter. I have a question 
regarding that. Most of the CIF files cell temperature are at 298 K, so if we 
use the structural data from that CIF (298 K) and run QE( after performing 
Optimizing atomic positions (relax.in), optimizing Unit cell 
(vc-relax.in)) to find electronic properties (e.g, density 
of states, fermi level), Are the output data of QE represent the temperature of 
0 K?

Thanks

Best
Md Jahid Hasan
PhD Student
University of Maine
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[QE-users] temperature of the output electronic properties in QE

[Md. Jahid Hasan Sagor]

Hi,

What's the temperature of the output electronic properties, even if we use
298 K cell info (atom position) as an input?
 Normally to prepare input file (structure of materials) for QE, I searched
the corresponding CIF file from this website (
http://www.crystallography.net/cod/result.php), after that I use Vesta to
get the relevant atomic positions and lattice parameter. I have a question
regarding that. Most of the CIF files cell temperature are at 298 K, so if
we use the structural data from that CIF (298 K) and run QE( after
performing Optimizing atomic positions (relax.in), optimizing Unit cell (
vc-relax.in)) to find electronic properties (e.g, density of states, fermi
level), Are the output data of QE represent the temperature of 0 K?

Thanks

Best
Md Jahid Hasan
PhD Student
University of Maine
___
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[QE-users] K_POINTS problem of band_interpolation.x

[Shuai Zhao]

Dear QE user,

I am studying the example of band_interpolation.x in the PP examples folder 
“~/qe-7.2/PP/examples/exx_interpolated_bands_example/pbe_fourier” 
I extract the pwscf.xml file directly from the filexml.tar.gz file using the 
tar commend. Then use the commend:

band_interpolation.x < fourier.in > fourier.out

and got this error:

PROGRAM: band_interpolation
k_points = none

%%
 Error in routine band_interpolation (1):
  K_POINTS card must be specified with tpiba_b
 %%

 stopping …

The input file fourier.in is directly used in the folder without any 
modification:


  method = 'fourier'
  miller_max = 7
/
ROUGHNESS
  3
  1.0d0  0.50d0  0.250d0
K_POINTS { tpiba_b }
  5
   L 20
   gG 20
   X 0
   1.0 1.0 0.0 30
   gG  1

Looking forward to hear a reply. Thanks in advance.

Best regards,

Shuai Zhao
Chongqing University of Technology 
P.R. China
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