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Today's Topics:
1. Re: Calculating U parameter for Ni in LiNiO2 using hp.x
(Timrov Iurii)
2. FFT grid problems with ph.x (Jakob Kraus)
3. Re: Atoms switching after certain time step in cp.x
(Abhirup Patra)
4. Re: FFT grid problems with ph.x (Paolo Giannozzi)
5. Regarding Surface passivation (Sai vishnu)
6. Query regarding k path selection, mismatching of band gap
(Poonam Kaushik)
7. Re: Query regarding k path selection, mismatching of band gap
(Nicola Marzari)
8. Re: Query regarding k path selection, mismatching of band gap
(Poonam Kaushik)
9. Re: Query regarding k path selection, mismatching of band gap
(Nicola Marzari)
10. Re: error while calculating InAs phonon dispersion with QE
6.5 (Paolo Giannozzi)
11. Re: error while calculating InAs phonon dispersion with QE
6.5 (Sheikh Ziauddin Ahmed)
12. Re: Query regarding k path selection, mismatching of band gap
(Poonam Kaushik)
13. Re: Query regarding k path selection, mismatching of band gap
(Vahid Askarpour)
14. Re: Query regarding k path selection, mismatching of band gap
(Poonam Kaushik)
15. Re: error while calculating InAs phonon dispersion with QE
6.5 (Paolo Giannozzi)
16. Re: Query regarding k path selection, mismatching of band gap
(Poonam Kaushik)
----------------------------------------------------------------------
Message: 1
Date: Tue, 13 Oct 2020 11:01:47 +0000
From: Timrov Iurii <iurii.tim...@epfl.ch>
To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org>
Subject: Re: [QE-users] Calculating U parameter for Ni in LiNiO2 using
hp.x
Message-ID: <0e316dd7bac24ca4a5d59fdcb4c74...@epfl.ch>
Content-Type: text/plain; charset="iso-8859-1"
Dear Mohammad,
There are 4 q points in hp.out:
Ok. I was looking at the old files that you shared and there were 6 q points.
Probably you have changed something in your PW input, and now you have more
symmetries and hence fewer q points.
To solve the convergence problem for the q point #4 I suggest to use
conv_thr_chi = 3.0d-5 instead of conv_thr_chi = 1.0d-5. Indeed, the residue for
q#4 is below 3.d-5 after 25 iterations:
atom # 1 q point # 4 iter # 25
chi: 1 -0.0982377516 residue: 0.0000065024
chi: 2 -0.0000089671 residue: 0.0000205352
chi: 3 -0.0000484762 residue: 0.0000067400
chi: 4 -0.0000000000 residue: 0.0000000000
chi: 5 -0.0000333051 residue: 0.0000117502
chi: 6 -0.0000089671 residue: 0.0000205352
chi: 7 0.0032070938 residue: 0.0000015134
chi: 8 -0.0000089671 residue: 0.0000205352
chi: 9 -0.0000333051 residue: 0.0000117502
chi: 10 0.0000000000 residue: 0.0000000000
chi: 11 -0.0000484762 residue: 0.0000067400
chi: 12 -0.0000089671 residue: 0.0000205352
Average number of iter. to solve lin. system: 30.0
Total CPU time : 85250.2 s
Greetings,
Iurii
--
Dr. Iurii TIMROV
Postdoctoral Researcher
STI - IMX - THEOS and NCCR - MARVEL
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: users <users-boun...@lists.quantum-espresso.org> on behalf of Mohammad Moaddeli
<mohammad.moadd...@gmail.com>
Sent: Tuesday, October 13, 2020 11:29:57 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Calculating U parameter for Ni in LiNiO2 using hp.x
Dear Iurii,
Thanks for your prompt reply.
A google drive link is provided:
https://drive.google.com/file/d/1-wXwPi5t4gSRBAilDT0ym5vOK8vxosif/view?usp=sharing
There are 4 q points in hp.out:
=-----------------------------------------------------------------
.
.
.
The grid of q-points ( 2, 2, 2) ( 4 q-points ) :
N xq(1) xq(2) xq(3) wq
1 0.000000000 0.000000000 0.000000000 0.125000000
2 0.000000000 0.000000000 -0.202041221 0.125000000
3 0.000000000 -0.577350269 0.000000000 0.375000000
4 0.000000000 -0.577350269 -0.202041221 0.375000000
=-----------------------------------------------------------------
Best,
Mohammad
ShirazU
On Tue, Oct 13, 2020 at 12:21 PM Timrov Iurii
<iurii.tim...@epfl.ch<mailto:iurii.tim...@epfl.ch>> wrote:
Dear Mohammad,
Based on your recommendations, everything went well for q point #3. However, q point #4 did not
converge. Required converging iterations from q point #1 to 3 is as following: 45 iterations for
q1, 63 iterations for q2, and 51 iterations for q3. q4 did not converge after 196 iterations. It
took 6 days. Finally I stopped hp.x because of fluctuation in "residue" for
"chi".
Did you use conv_thr_chi = 1.0d-5 and alpha_mix(1)= 0.05 for q#4 ? Can you
share your input and output files (PW and HP) via Google Drive?
Is it possible and reasonable to run hp.x for q point #1, 2, and 3 separately
and use sum_pertq=.true. as well as start_q=1, last_q=3, and
perturb_only_atom(1)=.true. to calculate the U parameter? (There are totally 4
q points)
I do not understand what you want to do. But I can tell that you cannot use
sum_pertq=.true. if you do not have all calculations for all q points done
(there are 6 q points in your case, not 4):
The grid of q-points ( 2, 2, 2) ( 6 q-points ) :
N xq(1) xq(2) xq(3) wq
1 0.000000000 0.000000000 0.000000000 0.125000000
2 1.747932183 1.009169115 -0.353154352 0.125000000
3 -0.000000002 -1.009169115 -0.176577175 0.250000000
4 1.747932182 0.000000000 -0.529731527 0.250000000
5 -0.873966092 -0.504584557 -0.353154351 0.125000000
6 0.873966092 0.504584557 -0.706308703 0.125000000
Greetings,
Iurii
--
Dr. Iurii TIMROV
Postdoctoral Researcher
STI - IMX - THEOS and NCCR - MARVEL
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: users
<users-boun...@lists.quantum-espresso.org<mailto:users-boun...@lists.quantum-espresso.org>>
on behalf of Mohammad Moaddeli
<mohammad.moadd...@gmail.com<mailto:mohammad.moadd...@gmail.com>>
Sent: Tuesday, October 13, 2020 8:25:12 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Calculating U parameter for Ni in LiNiO2 using hp.x
Dear Iurii,
Based on your recommendations, everything went well for q point #3. However, q point #4 did not
converge. Required converging iterations from q point #1 to 3 is as following: 45 iterations for
q1, 63 iterations for q2, and 51 iterations for q3. q4 did not converge after 196 iterations. It
took 6 days. Finally I stopped hp.x because of fluctuation in "residue" for
"chi".
Is it possible and reasonable to run hp.x for q point #1, 2, and 3 separately
and use sum_pertq=.true. as well as start_q=1, last_q=3, and
perturb_only_atom(1)=.true. to calculate the U parameter? (There are totally 4
q points)
alpha_mix is also reduced down to 0.01 as another alternative. It is still
running...
Any help will be greatly appreciated
Best,
Mohammad
ShirazU
On Fri, Sep 18, 2020 at 6:24 PM Timrov Iurii
<iurii.tim...@epfl.ch<mailto:iurii.tim...@epfl.ch>> wrote:
Dear Mohammad,
Your system seems to be delicate to converge. So I found that the mixing
parameter alpha_mix needs to be reduce further, down to 0.05 (which is very
small). With this, you can converge the HP calculation for the third q point
with the accuracy conv_thr_chi = 1.0d-5 (which is still fine).
By the way, if you want to test the convergence of the HP code for a specific q
point, you can use the input parameters start_q and last_q and specify for
which perturbed atom you do this. In your case, you need to specify the
following in the input for HP:
perturb_only_atom(1) = .true.
start_q = 3
last_q = 3
Here is the documentation: https://www.quantum-espresso.org/Doc/INPUT_HP.html
Also, when using iverbosity = 4 the HP code prints a lot of information in the
output. This is not really needed in this case. I would use iverbosity = 2.
Greetings,
Iurii
--
Dr. Iurii TIMROV
Postdoctoral Researcher
STI - IMX - THEOS and NCCR - MARVEL
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: users
<users-boun...@lists.quantum-espresso.org<mailto:users-boun...@lists.quantum-espresso.org>>
on behalf of Mohammad Moaddeli
<mohammad.moadd...@gmail.com<mailto:mohammad.moadd...@gmail.com>>
Sent: Friday, September 18, 2020 6:14:48 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Calculating U parameter for Ni in LiNiO2 using hp.x
Dear Iurii,
Unfortunately the q pont #3 did not converge. All input and output files are
available in this link:
https://drive.google.com/file/d/1zWoYq3kfBfH-6bw8s5llDm-BYFxM3ndQ/view?usp=sharing
Any help will be greatly appreciated.
Regards,
Mohammad
On Wed, Sep 16, 2020 at 1:00 PM Timrov Iurii
<iurii.tim...@epfl.ch<mailto:iurii.tim...@epfl.ch>> wrote:
Dear Mohammad,
By changing the threshold values you mentioned, nscf calculation finished (no
"cholesky" error)...
Great!
...but there is divergence in computing "chi".
The HP calculation for q points #1 and #2 has converged, but the problem is for
the q point #3. In the HP input, please setup
alpha_mix(1) = 0.1
and try again.
Also I suggest to use the default value nmix = 4, because I have never tried
changing it to something else (you are using nmix=5) and so I do not know what
to expect.
Also note that the parameter conv_thr_chi = 1.0d-8 is very tight, so can try
even something like conv_thr_chi = 1.0d-6 which should also be fine (because
your calculations take a lot of time with 16 cores that you use).
Greetings,
Iurii
--
Dr. Iurii TIMROV
Postdoctoral Researcher
STI - IMX - THEOS and NCCR - MARVEL
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: users
<users-boun...@lists.quantum-espresso.org<mailto:users-boun...@lists.quantum-espresso.org>>
on behalf of Mohammad Moaddeli
<mohammad.moadd...@gmail.com<mailto:mohammad.moadd...@gmail.com>>
Sent: Wednesday, September 16, 2020 7:21:53 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Calculating U parameter for Ni in LiNiO2 using hp.x
Dear Iurii,
By changing the threshold values you mentioned, nscf calculation finished (no "cholesky"
error), but there is divergence in computing "chi". Please find the link below. All input
and output files are attached.
https://drive.google.com/file/d/1TWDQ3X_jG7HsgaVvhUiu3oVWt28g3DNz/view?usp=sharing
Best,
Mohammad
ShirazU
On Sun, Sep 13, 2020 at 2:13 PM Timrov Iurii
<iurii.tim...@epfl.ch<mailto:iurii.tim...@epfl.ch>> wrote:
Dear Mohammad,
1.In the SCF input for the supercell you have:
conv_thr = 1.0d-20
This is extremely low! Try some value in-between 1.0d-10 and 1.d-15.
2.In the HP input for the supercell you have:
ethr_nscf = 1.D-14
This is also extremely low! Try the default value of 1.0d-11.
If you still have a problem when using e.g. conv_thr=1.d-10 and
ethr_nscf=1.d-11 then please put input and output files on Google Drive or
Dropbox and send a link to us (do not forget to check the permissions of the
shared folder).
HTH
Iurii
--
Dr. Iurii TIMROV
Postdoctoral Researcher
STI - IMX - THEOS and NCCR - MARVEL
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334
________________________________
From: users
<users-boun...@lists.quantum-espresso.org<mailto:users-boun...@lists.quantum-espresso.org>>
on behalf of Mohammad Moaddeli
<mohammad.moadd...@gmail.com<mailto:mohammad.moadd...@gmail.com>>
Sent: Sunday, September 13, 2020 6:12:27 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Calculating U parameter for Ni in LiNiO2 using hp.x
Dear Lorenzo,
Thank you for your prompt reply.
Using qe_6.6 (in which calculating force and stress is implemented) the 221
supercell relaxed with the U obtained from the output of hp.x for the primitive
cell, but the same error appeared. What do you recommend?
Best,
Mohammad,
ShirazU
On Mon, Sep 7, 2020 at 12:07 PM Lorenzo Paulatto
<paul...@gmail.com<mailto:paul...@gmail.com>> wrote:
> I am trying to calculate the U parameter for Ni in LiNiO2. The hp.x
> (qe_6.5) runs without any error for the primitive cell, however the
> "problems computing cholesky" error occurs for running a 2?2?1 supercell
The most likely cause is that you did a mistake in the atomic position
or cell size.
kind regards
--
Lorenzo Paulatto - Paris
_______________________________________________
Quantum ESPRESSO is supported by MaX
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Message: 2
Date: Tue, 13 Oct 2020 14:55:07 +0200
From: Jakob Kraus <jakob.kr...@physik.tu-freiberg.de>
To: users@lists.quantum-espresso.org
Subject: [QE-users] FFT grid problems with ph.x
Message-ID:
<85cf6fd6-4b4b-e43a-208e-12c76f3f1...@physik.tu-freiberg.de>
Content-Type: text/plain; charset=utf-8; format=flowed
Dear QE community,
my phonon calculation for AlN complains about
"Error in routine scale_sym_ops (4): incompatible FFT grid"
, whereas the scf calculation I performed beforehand went through
without any problems.
I've consulted the user guide and tried increasing the cutoffs for
wavefunction and density, to no avail.
Additionally, I've tried playing around with the lattice constants and
setting the FFT grid by hand, to numbers
that are divisible by 12, which did not help either.
Do you have any idea that could help me? I am pretty much stuck at this
point.
Below is the original espresso.pwi input file for the scf calculation
that is performed before the phonon calculation.
Yours sincerely,
Jakob Kraus (Technische Universit?t Bergakademie Freiberg)
&CONTROL
?? calculation????? = 'scf'
?? title??????????? = 'AlN_vib'
?? verbosity??????? = 'high'
?? restart_mode???? = 'from_scratch'
?? tstress????????? = .true.
?? tprnfor????????? = .true.
?? outdir?????????? = './'
?? prefix?????????? = 'espresso'
?? pseudo_dir?????? = '/home/kraus/theos_pp/pz.0.3.1/PSEUDOPOTENTIALS_NC'
/
&SYSTEM
?? ibrav??????????? = 4
?? ecutwfc????????? = 190
?? occupations????? = 'fixed'
?? nspin??????????? = 1
?? ntyp???????????? = 2
?? nat????????????? = 4
?? celldm(1)??????? = 5.877048275900463
?? celldm(3)??????? = 1.6012861736334407
/
&ELECTRONS
?? electron_maxstep = 300
?? conv_thr???????? = 1e-10
?? mixing_beta????? = 0.7
/
&IONS
/
&CELL
/
ATOMIC_SPECIES
Al 26.9815385 Al.pz-n-nc.UPF
N 14.007 N.pz-nc.UPF
K_POINTS automatic
5 5 5? 0 0 0
ATOMIC_POSITIONS angstrom
Al 1.5550015550 0.8977787708 0.0000000000
Al -0.0000015550 1.7955602350 2.4900000000
N 1.5550015550 0.8977787708 1.9028580000
N -0.0000015550 1.7955602350 4.3928580000
------------------------------
Message: 3
Date: Tue, 13 Oct 2020 11:48:53 -0400
From: Abhirup Patra <abhir...@sas.upenn.edu>
To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org>
Subject: Re: [QE-users] Atoms switching after certain time step in
cp.x
Message-ID:
<CAJ=Ovub-pa6mT=fFBiRaC0KAPGxVW59Pf1wYS1UpcCS=blm...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Paolo,
Thanks, for your reply, it makes sense to me now.
Abhirup
----------------------------------------------------------------------------------------------
Abhirup Patra
Department of Chemistry
University of Pennsylvania
On Tue, Oct 13, 2020 at 4:04 AM Paolo Giannozzi <p.gianno...@gmail.com>
wrote:
QE doesn't switch atoms as far as I know. Visualizers occasionally do:
their algorithms sometimes cannot decide whether to visualize an atom or
its periodic image and so you see atoms at the border of a box that
disappear at one side and appear at the other side. If this is the case,
there isn't anything wrong (but there isn't much that one can do either)
Paolo
On Tue, Oct 13, 2020 at 6:49 AM Abhirup Patra <abhir...@sas.upenn.edu>
wrote:
Dear QE users and developers,
Recently, I have performed some NVT simulation using cp.x for a molecule
on surface reaction, however, it looks like that after the 100-th step,
atoms in the molecule switch position with the atom of the bottom-most
metallic layer of the slab and then go back to the surface again after nth
time-step.
I have converted .pos and .cel files to .xsf file using cppp.x with
QE.6.6 compiled with -D__OLDXML and visualized the xsf file in Xcrysden. My
input geometry is fine, meaning, nothing is switched after ionic
relaxation.
Any suggestions or tips about what might be the reason for this behavior?
Thanks,
Abhirup
----------------------------------------------------------------------------------------------
Abhirup Patra
Department of Chemistry
University of Pennsylvania
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
_______________________________________________
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users mailing list users@lists.quantum-espresso.org
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Message: 4
Date: Tue, 13 Oct 2020 18:18:37 +0200
From: Paolo Giannozzi <p.gianno...@gmail.com>
To: Quantum ESPRESSO users Forum <users@lists.quantum-espresso.org>
Subject: Re: [QE-users] FFT grid problems with ph.x
Message-ID:
<CAPMgbCtgaKT=8e+o9koaxgeyn_uibkvzrqy8jmep-wg0atg...@mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
I think the problem (and the fix) is the same as here:
https://gitlab.com/QEF/q-e/-/merge_requests/1069
Paolo
On Tue, Oct 13, 2020 at 2:55 PM Jakob Kraus <
jakob.kr...@physik.tu-freiberg.de> wrote:
Dear QE community,
my phonon calculation for AlN complains about
"Error in routine scale_sym_ops (4): incompatible FFT grid"
, whereas the scf calculation I performed beforehand went through
without any problems.
I've consulted the user guide and tried increasing the cutoffs for
wavefunction and density, to no avail.
Additionally, I've tried playing around with the lattice constants and
setting the FFT grid by hand, to numbers
that are divisible by 12, which did not help either.
Do you have any idea that could help me? I am pretty much stuck at this
point.
Below is the original espresso.pwi input file for the scf calculation
that is performed before the phonon calculation.
Yours sincerely,
Jakob Kraus (Technische Universit?t Bergakademie Freiberg)
&CONTROL
calculation = 'scf'
title = 'AlN_vib'
verbosity = 'high'
restart_mode = 'from_scratch'
tstress = .true.
tprnfor = .true.
outdir = './'
prefix = 'espresso'
pseudo_dir = '/home/kraus/theos_pp/pz.0.3.1/PSEUDOPOTENTIALS_NC'
/
&SYSTEM
ibrav = 4
ecutwfc = 190
occupations = 'fixed'
nspin = 1
ntyp = 2
nat = 4
celldm(1) = 5.877048275900463
celldm(3) = 1.6012861736334407
/
&ELECTRONS
electron_maxstep = 300
conv_thr = 1e-10
mixing_beta = 0.7
/
&IONS
/
&CELL
/
ATOMIC_SPECIES
Al 26.9815385 Al.pz-n-nc.UPF
N 14.007 N.pz-nc.UPF
K_POINTS automatic
5 5 5 0 0 0
ATOMIC_POSITIONS angstrom
Al 1.5550015550 0.8977787708 0.0000000000
Al -0.0000015550 1.7955602350 2.4900000000
N 1.5550015550 0.8977787708 1.9028580000
N -0.0000015550 1.7955602350 4.3928580000
_______________________________________________
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing list users@lists.quantum-espresso.org
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