Re: [QE-users] QE as a library

[Lorenzo Paulatto]

I would add to what Paolo said, that many people have sort of done it 
already. Also note, that things become exponentially more difficult when 
you include levels of parallelization, gpu support, etc.


Some examples:

Plumed (https://www.plumed.org/) can use QE as a library, although 
because of teh rigidity of the system it tends to lag behind many 
versions in compatibility


Python ASE (https://wiki.fysik.dtu.dk/ase/) can call the QE binary and 
parse the results. Not really "like a library" but it depends what you 
want to do in practive


Python QePY (https://pypi.org/project/qepy/) rewrites a few of QS 
subroutines in python and uses some others like a library.


iPi (https://ipi-code.org/i-pi/getting-started.html) controls remotely a 
running instance of QE.


I'm sure there are others.

cheers



On 23/04/2024 22:14, Paolo Giannozzi wrote:

On 23/04/2024 10:10, Alireza Ghasemi wrote:

   Can QE be called as a library? For example, a small program that 
provides a structure to a QE routine and the routine returns energy 
and forces, or possibly more than these two quantities?
it can, sort of. There are routines that perform a specific task, but 
they typically need quite a bit of initialization to work. It depends 
a lot upon what you want to achieve and which level of granularity in 
calling QE routines you need, or desire


Paolo

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Re: [QE-users] [SPAM] nscf calculation error

[Lorenzo Paulatto]

I had this sort of errors with the flang-based compilers, maybe the new 
Intel ifx could also cause this ?



On 3/25/24 11:05, Paolo Giannozzi wrote:
I am afraid (for you) that the origin of your problem is in your 
compiler. There is nothing wrong in your xml file: it looks exactly 
like the one that I generate and subsequently read


Paolo
On 3/25/24 09:33, Максим Кузнецов wrote:

25.03.2024, 11:02, "Paolo Giannozzi" :

    I don't see how what you describe may happen, unless:
    - you are reading data files produced by earlier code versions, or
    - you are using some exotic, little-tested option.
    Please provide the input data and maybe also the xml data 
produced in

    the scf run

    Paolo

    On 3/24/24 19:30, Максим Кузнецов wrote:


  Dear users,
  I encountered the following problem:
  sсf calculation works correctly, but when I try to run nscf
    calculation
  I get the following error:
     Atomic positions and unit cell read from directory:
        ./out/KFeS2.save/
        Message from routine qes_read:symmetriesType:
        error reading nsym
   
%%
        Error in routine qes_read: matrixType (10):
        required attribute rank not found, can't read further,
    stopping
   
%%
  However all tests in test-suite passed.
  QE version 7.3.1
  I'll be very grateful for reply!



  Sincerely,
  Kuznetsov Maksim,
  Masters student,
  Kazan Federal University.

    --
    Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
    Univ. Udine, via delle Scienze 208, 33100 Udine Italy, 
+39-0432-558216


  Sincerely,
  Kuznetsov Maksim,
  Masters student,
  Kazan Federal University.



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Re: [QE-users] open_grid.x with ibrav =4 error

[Lorenzo Paulatto]

After generating k points grid with open_grid.x, when i do pw2wan, i
encounter an error  like
  numk= 144  iknum=  38


This could happen if the list of k-points that you provide to 
"wannier90.x -pp" is not the same that was produced by open_grid.x


Did you copy the list of k-points printed from open_grid.x verbatim into 
the input of wannier90, and only afterward run "wannier90.x -pp" ?


hth

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Re: [QE-users] Convergence not achieved in 'relax' calculation

[Lorenzo Paulatto]

Hello Prasad,

it is the scf calculation that is not convergence, the fact that you are 
doing a "relax" is not relevant in this case. Because you are using 
DFT+U, this is unfortunately often the case. The usual reccomendations 
apply: 
https://www.quantum-espresso.org/Doc/pw_user_guide/node21.html#SECTION000600200


Also, you may try to set a reasonable number for electron_maxstep (i.e. 
50) and set scf_must_converge to false, it is possible that once the 
structure is partially relaxed convergence becomes easier.


hth


On 3/20/24 04:32, PRASAD SANKALPA WANNINAYAKA wrote:

Dear users,
I am studying the properties of Ilmenite using Quantum Espresso 7.2. I 
have performed a relax calculation for the ilmenite structure but 
after 400 iterations convergence is not achieved. I have restarted 
those calculations again but have not achieved convergence.


I have attached the input file with this mail. Would you be able to 
advise on the recommended approach to solve this problem?
output files: 
https://drive.google.com/drive/folders/1zyTNVXheas--C0sO7Mcnq-WnAPnH7O9j?usp=sharing


Kind regards,

Prasad



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Re: [QE-users] What to modify in "dynamics_module.f90" for making constant zero pressure during NVT simulation(pw.x)

[Lorenzo Paulatto]

On 16/03/2024 12:17, Jayraj Anadani wrote:

hello Paulatto,
but in cell_dynamics all options for pressure control are for vc-md 
and vc-relax. and i want to control pressure during 
ion_temperature=reduce-T option.


Dear Jayraj,

it is not very clear what you want to do. You can have constant NVT, or 
NVE or NPT, or NPE. But it looks to me that you want constant 
instantaneous P and V, which is impossible as P is a macroscopic 
quantity, it only makes sense on average.


kind regards




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Re: [QE-users] What to modify in "dynamics_module.f90" for making constant zero pressure during NVT simulation(pw.x)

[Lorenzo Paulatto]

Dear Anadani,
Check the cell_dynamics input variable and related. 



Kind regards.



On March 16, 2024 10:51:01 AM GMT+01:00, Jayraj Anadani 
 wrote:
>Hello QE community,
>I am performing an AIMD simulation of metallic alloys and encountering huge
>pressure(~50 to -50 Kbar) fluctuations, i wanted to set pressure around
>zero during NVT simulations with temperature reduction(reduce -T)or
>rescaling. Currently, I'm manually adjusting the box size after each
>certain MD steps (nstep-200) to fix this. Is there an automated way to
>maintain constant zero pressure?  The barasat is available for NPT
>simulation but i am using "reduce -T" option so i can't do NPT simulation
>way.
>Or i can change some part of script in "dynamics_module.f90".
>
>Thanks
>Regards
>
>Jayraj Anadani
>SPU Research scholar
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Re: [QE-users] Ayuda con calulos de ZPL, usando DeltaSCF

[Lorenzo Paulatto]

On 3/4/24 06:20, Wilber Muriel wrote:
"occupations='from_input' " and "occupations='from_input' " and 
"occupations='from_input' ". 



Well, you only need to set it once. However, note that this option is 
only supposed to be used with a single k-point. I do not think it works 
with more than one 9apart from being very cumbersome to use)




OCCUPATIONS
1.0 1.0 . 0.0 0.0. spin up
1.0 1.0 . 0.0 0.0. spin down




I would like to know: By specifying the two options mentioned above, 
the order of the orbitals remains unchanged during the whole 
optimization process?



No, the orbitals do what they want with the aim to minimize the total 
energy, and the fact that the eigenvalues are sorted in increasing order 
of energy.





Is it necessary to use some specific diaginalization algorithm?

Is it necessary to specify any other option?



Not that I know, I'm also note sure it will work the way you are trying 
to do. I recommend you try to reproduce some simple literature case first.


cheers




If any user can provide me with a tutorial, I would be very grateful.

Thank you for your attention


Wilver M.
PhD Student in Physics
University Of Chile

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Re: [QE-users] changing cell size 1x1 to 3x3 does not provide same DOS & BS

[Lorenzo Paulatto]

Dear Wenusara,

the 3x3 supercell has a much larger amount of vacuum, this is a typical 
source of problems with graphene, as one electron may like to wonder out 
in the vacuum.  Sticking to 5-10Å of vacuum is enough and should work 
fine, i.e. when you multiply celldm(1) by 3, you should also divide 
celldm(3) by the same amount to keep vacuum constant. Also, your plane 
wave cutoff seems a bit low, I assume you have tested convergence properly.


kind regards

On 23/02/2024 17:48, wenusaras wrote:

hi,

I am new to QE.
I start with the simple pw scf code of graphene 1x1 unit cell (i.e. 
nat=2) then the DOS and BS was obtained.
After that pw scf code was changed to 3x3 cell (i.e. nat =18) then the 
obtained DOS and BS was not similar to 1x1 (changing the number of 
kpoints was not make two BS (or DOS) similar).


Herewith I have attached the both pw scf & nscf files.

I am curious to know what is the reason for this?
Is there a way to make this both DOS and BS for both 1x1 and 3x3 to 
similar?



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Re: [QE-users] Different results for charged cluster in PHonon 5.1 and 7.2

[Lorenzo Paulatto]

Hello,

On top of what Paola says, I would recommend checking the output of pw.x 
first. If the total energy calculation is not identical, the phonons 
results will be widely different. And if there is a difference in the 
total energy calculation, it could be traced back more easily to a 
change in the code.


kind regards.


On 14/02/2024 11:14, RABONE Jeremy wrote:


Hello,


  I have re-run a Phonon calculation for a charged cluster that was 
done using version 5.1 with version 7.2 and the results are completely 
different; there is a large positive shift in the frequencies. Can 
somebody tell me what was done differently in 5.1 for charged cells ?



Kind regards,


Jeremy Rabone


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Re: [QE-users] Phonon calculation does not converge

[Lorenzo Paulatto]

The calculation is not only not converging, it is actually diverging. 
Changing alpha_mix and increasing nmix_ph can help, but it may also 
indicate something wrong with the calculation. I.e. a metal treated as 
semiconductor, or a ghost in the pseudopotential (which may be likely if 
you use norm-conservig cutoff with an ultrasoft dataset)


hth


On 1/23/24 08:47, Chirantan Pramanik wrote:

Hello All,

I was running Phonon for a few systems of carbonate minerals for a 
long time. Recently I used SSSP pseudopotential for PBE and faced a 
problem like the one pasted below. Optimization and SCF calculations 
are properly done. But phonon calculation is not converging. Please 
help. I think changing alpha_mix can be useful, but for my stable and 
optimized system, it should converge easily.


section from ph.x output:

 iter #  97 total cpu time :  1799.1 secs   av.it.:  84.0
    thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  1.595E+08

    iter #  98 total cpu time :  1822.7 secs   av.it.:  92.0
    thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  3.870E+10

    iter #  99 total cpu time :  1846.5 secs   av.it.:  92.0
    thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  4.585E+10

    iter # 100 total cpu time :  1869.3 secs   av.it.:  88.0
    thresh= 1.000E-02 alpha_mix =  0.700 |ddv_scf|^2 =  5.897E+09

   End of self-consistent calculation

   No convergence has been achieved


Please help in this regard.

Thanks and Regards,
Chirantan

Chirantan Pramanik
Postdoctoral Researcher
Dept. of Earth and Planetary Sciences
Weizmann Institute of Science
Rehovot, Israel

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Re: [QE-users] Requested some guidelines in First-principles molecular dynamics

[Lorenzo Paulatto]

p.s. Have a look at 
https://journals.aps.org/prb/pdf/10.1103/PhysRevB.94.075125 where the 
temperature dependent spectrum is in fact computed from the RMS


hth

On 1/11/24 04:46, Md. Jahid Hasan Sagor wrote:

Hi Dr. Paulatto,

Thank you so much for your comments.

Actually, The paper ( https://doi.org/10.1103/PhysRevB.77.125218 ) 
extracted the temperature of each configuration from the mean square 
displacement per atom of the configuration (GaAs). In the harmonic 
approximation, they determined the relationship between mean square 
displacement and temperature T from the phonon density of states of 
bulk GaAs calculated by Giannozzi et al. The equation as follows:


image.png
Here is the figure they generated
image.png


So, now If I can find out the RMS of GaAs using CPMD, I will try to 
observe the corresponding configuration of GaAs atoms. Finally, the 
atomic positions will be the input of Quantum Espresso pw.x etc ( I 
mean normally how do we calculate dielectric constant in QE).


Can I use  it ( https://anharmonic.github.io/thermal2/#d3_r2qx-code) 
for the same purpose?


Best
Hasan

On Wed, Jan 10, 2024 at 3:13 PM Lorenzo Paulatto 
 wrote:


I would guess that you calculate the static dielectric constant at
the temperature-dependent volume (experimental, or quasi-harmonic)
and you are 90% of the way there. Do you have a specific reason to
believe that it would be proportional to the RMS ?

Btw, the code d3_r2q.x included with the "anharmonic" package can
compute the RMS from an inexpensive phonon calculation, maybe have
a look at it before doing a large supercell MD.

https://anharmonic.github.io/thermal2/#d3_r2qx-code

cheers

On 10/01/2024 19:35, Md. Jahid Hasan Sagor wrote:

Actually, I have to calculate Dielectric constant for GaAs for
different temperatures (not 0 k). To do that, I need to extract
atomic positions for different RMS using CPMD. If anyone know
someone/ or give some guidelines, it would be great help for me.

Thank you.

On Tue, Jan 9, 2024, 2:09 PM Md. Jahid Hasan Sagor
 wrote:

Dear QE community,

I want to calculate the mean square displacement of GaAs
using CPMD. From the mean square displacement, I want to
extract the configuration of atoms (e.g atomic position of Ga
and As). Could anyone please give me some guidelines on how I
can perform it? Should I use only the cp.x package or by
other means? Your time and suggestions would be a great help
for me.

Best Regards
Md Jahid Hasan
PhD Student, Mechanical Engineering
University of Maine


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Re: [QE-users] Requested some guidelines in First-principles molecular dynamics

[Lorenzo Paulatto]

On 1/11/24 20:57, Md. Jahid Hasan Sagor wrote:

Hi Dr. Paulatto,

Thank you for your advice. I also like your idea about epsilon.x. But 
the dielectric function we get using epsilon.x (QE), Isn't it for only 
0 K? How can I extend it to another temperature?


It is computed with an electronic temperature of 0K, but it is exactly 
the same as in the paper you are trying to reproduce. But this is not a 
big deal, there is very little direct effect of temperature on 
electrons: compare the energy of thermal excitation (k_B T) with the 
band gap of GaAs and you will see why. I.e. electron orbitals are far 
too rigid to be affected by temperature, especially in insulators. Even 
in metal we use fictitious electronic temperature to speed up 
integration (aka smearing) that is of the order of 1'000K, and it does 
not change the electronic structure much. The effect only come through 
the motion of ions, so move the ions and you got finite temperature.


But do not believe me: change the electronic occupation to "smearing" 
and set a Fermi-Dirca smearing which is equivalent to the temperature 
you want (it is in Ry, i.e. 1 Ry = 157'887 K). Then see how, much the 
total energy and band structure change. how many k-points do you need to 
have a discernible Fermi surface at the to of valence band, etc.


hth




Best
Md Jahid

On Thu, Jan 11, 2024 at 2:36 PM Lorenzo Paulatto 
 wrote:



On 11/01/2024 20:06, Md. Jahid Hasan Sagor wrote:

Hi Dr. Paulatto,

Thank you so much for your suggestions. I was going in the wrong
direction. So if I use your recommended code
(https://anharmonic.github.io/thermal2/#d3_r2qx-code), would I be
able to generate the following figure for Bulk GaAs?


No. The anharmonic code is about vibrational properties.



Actually my main goal is to calculate dielectric function at
different temperatures (not 0 K).


You can try to do like in the paper. Or you can try a different
approach, i.e. replacing the sampling via molecular dynamics with
a stochastic sampling, like the one provided by the SSCHA code
http://sscha.eu/, which is also compatible with QE. Anyway, the
supercell they use is tiny (8 atoms, which is just the
simple-cubic form of GaAs), you should be able to use the
epsilon.x code that comes with QE (check the manual in
PP/Doc/man_eps.pdf). I would say, start with just epsilon as a
function of the volume, test convergence and see if you can afford
it,.

kind regards




Thanks
Md Jahid Hasan

On Thu, Jan 11, 2024 at 9:19 AM Lorenzo Paulatto
 wrote:

Hello Jahid,

I have read the article very quickly, but I do not think they
use the RMS to compute epsilon. All they do is compute
epsilon for a few sample atomic potisions reached during the
MD run, then they average it. The "Theoretical Method"
section does not have any logic, but it is explained in the
"Conclusions". The RMS seems to be only used to ascertain the
validity of the simulation.

hth

On 1/11/24 04:42, Md. Jahid Hasan Sagor wrote:

Hi Dr. Paulatto,

Thank you so much for your comments.

Actually, The paper (attached) extracted the temperature of
each configuration from the mean square displacement per
atom of the configuration (GaAs). In the harmonic
approximation, they determined the relationship between 
mean square displacement and temperature T from the phonon
density of states of bulk GaAs calculated by Giannozzi et
al. The equation as follows:

image.png
Here is the figure they generated
image.png

So, now If I can find out the RMS of GaAs using CPMD, I will
try to observe the corresponding configuration of GaAs
atoms. Finally, the atomic positions will be the input of
Quantum Espresso pw.x etc ( I mean normally how do we
calculate dielectric constant in QE).

Can I use  it (
https://anharmonic.github.io/thermal2/#d3_r2qx-code) for the
same purpose?

Best
Hasan

On Wed, Jan 10, 2024 at 3:13 PM Lorenzo Paulatto
 wrote:

I would guess that you calculate the static dielectric
constant at the temperature-dependent volume
(experimental, or quasi-harmonic) and you are 90% of the
way there. Do you have a specific reason to believe that
it would be proportional to the RMS ?

Btw, the code d3_r2q.x included with the "anharmonic"
package can compute the RMS from an inexpensive phonon
calculation, maybe have a look at it before doing a
large supercell MD.

https://anharmonic.github.io/thermal2/#d3_r2qx-code

cheers

On 10/01/2024 19:35, Md. Jahid Hasan Sagor wrote:

Actually,

Re: [QE-users] Requested some guidelines in First-principles molecular dynamics

[Lorenzo Paulatto]

On 11/01/2024 20:06, Md. Jahid Hasan Sagor wrote:

Hi Dr. Paulatto,

Thank you so much for your suggestions. I was going in the wrong 
direction. So if I use your recommended code 
(https://anharmonic.github.io/thermal2/#d3_r2qx-code), would I be able 
to generate the following figure for Bulk GaAs?


No. The anharmonic code is about vibrational properties.



Actually my main goal is to calculate dielectric function at different 
temperatures (not 0 K).


You can try to do like in the paper. Or you can try a different 
approach, i.e. replacing the sampling via molecular dynamics with a 
stochastic sampling, like the one provided by the SSCHA code 
http://sscha.eu/, which is also compatible with QE. Anyway, the 
supercell they use is tiny (8 atoms, which is just the simple-cubic form 
of GaAs), you should be able to use the epsilon.x code that comes with 
QE (check the manual in PP/Doc/man_eps.pdf). I would say, start with 
just epsilon as a function of the volume, test convergence and see if 
you can afford it,.


kind regards




Thanks
Md Jahid Hasan

On Thu, Jan 11, 2024 at 9:19 AM Lorenzo Paulatto 
 wrote:


Hello Jahid,

I have read the article very quickly, but I do not think they use
the RMS to compute epsilon. All they do is compute epsilon for a
few sample atomic potisions reached during the MD run, then they
average it. The "Theoretical Method" section does not have any
logic, but it is explained in the "Conclusions". The RMS seems to
be only used to ascertain the validity of the simulation.

hth

On 1/11/24 04:42, Md. Jahid Hasan Sagor wrote:

Hi Dr. Paulatto,

Thank you so much for your comments.

Actually, The paper (attached) extracted the temperature of each
configuration from the mean square displacement per atom of the
configuration (GaAs). In the harmonic approximation, they
determined the relationship between  mean square displacement and
temperature T from the phonon density of states of bulk GaAs
calculated by Giannozzi et al. The equation as follows:

image.png
Here is the figure they generated
image.png

So, now If I can find out the RMS of GaAs using CPMD, I will try
to observe the corresponding configuration of GaAs atoms.
Finally, the atomic positions will be the input of Quantum
Espresso pw.x etc ( I mean normally how do we calculate
dielectric constant in QE).

Can I use  it (
https://anharmonic.github.io/thermal2/#d3_r2qx-code) for the same
purpose?

Best
Hasan

On Wed, Jan 10, 2024 at 3:13 PM Lorenzo Paulatto
 wrote:

I would guess that you calculate the static dielectric
constant at the temperature-dependent volume (experimental,
or quasi-harmonic) and you are 90% of the way there. Do you
have a specific reason to believe that it would be
proportional to the RMS ?

Btw, the code d3_r2q.x included with the "anharmonic" package
can compute the RMS from an inexpensive phonon calculation,
maybe have a look at it before doing a large supercell MD.

https://anharmonic.github.io/thermal2/#d3_r2qx-code

cheers

On 10/01/2024 19:35, Md. Jahid Hasan Sagor wrote:

Actually, I have to calculate Dielectric constant for GaAs
for different temperatures (not 0 k). To do that, I need to
extract atomic positions for different RMS using CPMD. If
anyone know someone/ or give some guidelines, it would be
great help for me.

Thank you.

On Tue, Jan 9, 2024, 2:09 PM Md. Jahid Hasan Sagor
 wrote:

Dear QE community,

I want to calculate the mean square displacement of GaAs
using CPMD. From the mean square displacement, I want to
extract the configuration of atoms (e.g atomic position
of Ga and As). Could anyone please give me some
guidelines on how I can perform it? Should I use only
the cp.x package or by other means? Your time and
suggestions would be a great help for me.

Best Regards
Md Jahid Hasan
PhD Student, Mechanical Engineering
University of Maine


___
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country and on the free and peaceful scientific, cultural,
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-- 
Dr. Lorenzo Paulatto

Id

Re: [QE-users] Requested some guidelines in First-principles molecular dynamics

[Lorenzo Paulatto]

Hello Jahid,

I have read the article very quickly, but I do not think they use the 
RMS to compute epsilon. All they do is compute epsilon for a few sample 
atomic potisions reached during the MD run, then they average it. The 
"Theoretical Method" section does not have any logic, but it is 
explained in the "Conclusions". The RMS seems to be only used to 
ascertain the validity of the simulation.


hth

On 1/11/24 04:42, Md. Jahid Hasan Sagor wrote:

Hi Dr. Paulatto,

Thank you so much for your comments.

Actually, The paper (attached) extracted the temperature of each 
configuration from the mean square displacement per atom of the 
configuration (GaAs). In the harmonic approximation, they determined 
the relationship between mean square displacement and temperature T 
from the phonon density of states of bulk GaAs calculated by Giannozzi 
et al. The equation as follows:


image.png
Here is the figure they generated
image.png

So, now If I can find out the RMS of GaAs using CPMD, I will try to 
observe the corresponding configuration of GaAs atoms. Finally, the 
atomic positions will be the input of Quantum Espresso pw.x etc ( I 
mean normally how do we calculate dielectric constant in QE).


Can I use  it ( https://anharmonic.github.io/thermal2/#d3_r2qx-code) 
for the same purpose?


Best
Hasan

On Wed, Jan 10, 2024 at 3:13 PM Lorenzo Paulatto 
 wrote:


I would guess that you calculate the static dielectric constant at
the temperature-dependent volume (experimental, or quasi-harmonic)
and you are 90% of the way there. Do you have a specific reason to
believe that it would be proportional to the RMS ?

Btw, the code d3_r2q.x included with the "anharmonic" package can
compute the RMS from an inexpensive phonon calculation, maybe have
a look at it before doing a large supercell MD.

https://anharmonic.github.io/thermal2/#d3_r2qx-code

cheers

On 10/01/2024 19:35, Md. Jahid Hasan Sagor wrote:

Actually, I have to calculate Dielectric constant for GaAs for
different temperatures (not 0 k). To do that, I need to extract
atomic positions for different RMS using CPMD. If anyone know
someone/ or give some guidelines, it would be great help for me.

Thank you.

On Tue, Jan 9, 2024, 2:09 PM Md. Jahid Hasan Sagor
 wrote:

Dear QE community,

I want to calculate the mean square displacement of GaAs
using CPMD. From the mean square displacement, I want to
extract the configuration of atoms (e.g atomic position of Ga
and As). Could anyone please give me some guidelines on how I
can perform it? Should I use only the cp.x package or by
other means? Your time and suggestions would be a great help
for me.

Best Regards
Md Jahid Hasan
PhD Student, Mechanical Engineering
University of Maine


___
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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
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu  
<http://www.max-centre.eu>)
users mailing listus...@lists.quantum-espresso.org
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-- 
Dr. Lorenzo Paulatto

IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05
___
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country and on the free and peaceful scientific, cultural,
and economic cooperation amongst peoples
___
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<http://www.max-centre.eu>)
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https://lists.quantum-espresso.org/mailman/listinfo/users


--
Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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
___

Re: [QE-users] Requested some guidelines in First-principles molecular dynamics

[Lorenzo Paulatto]

I would guess that you calculate the static dielectric constant at the 
temperature-dependent volume (experimental, or quasi-harmonic) and you 
are 90% of the way there. Do you have a specific reason to believe that 
it would be proportional to the RMS ?


Btw, the code d3_r2q.x included with the "anharmonic" package can 
compute the RMS from an inexpensive phonon calculation, maybe have a 
look at it before doing a large supercell MD.


https://anharmonic.github.io/thermal2/#d3_r2qx-code

cheers

On 10/01/2024 19:35, Md. Jahid Hasan Sagor wrote:
Actually, I have to calculate Dielectric constant for GaAs for 
different temperatures (not 0 k). To do that, I need to extract atomic 
positions for different RMS using CPMD. If anyone know someone/ or 
give some guidelines, it would be great help for me.


Thank you.

On Tue, Jan 9, 2024, 2:09 PM Md. Jahid Hasan Sagor 
 wrote:


Dear QE community,

I want to calculate the mean square displacement of GaAs using
CPMD. From the mean square displacement, I want to extract the
configuration of atoms (e.g atomic position of Ga and As). Could
anyone please give me some guidelines on how I can perform it?
Should I use only the cp.x package or by other means? Your time
and suggestions would be a great help for me.

Best Regards
Md Jahid Hasan
PhD Student, Mechanical Engineering
University of Maine


___
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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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--
Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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and economic cooperation amongst peoples
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Re: [QE-users] Calculating Dielectric Constant

[Lorenzo Paulatto]

Dear Elham,

the static dielectric constant is computed by the phonon (ph.x) code in 
non-metallic crystals, just by setting epsil=.true.


See for example, step 7 of example 1 therein (PHonon/examples/example01)


If you want the electronic or phononic contribution to the complex 
frequency-dependent dielectric matrix, it is another story. You can do 
the former with epsilon.x (PP/Doc/eps_man.pdf) and the latter with the 
"anharmonic" code package that I develop (https://anharmonic.github.io/) 
both calculations are way more complex and require a bit of studying. 
Other methods are also available.



hth


On 08/01/2024 21:19, Elham Rezaee wrote:


Dear Quantum ESPRESSO Users,

 I am currently working on a project that requires the calculation of 
the dielectric constant of a material, and I would like to use Quantum 
ESPRESSO for this purpose.


I am reaching out to the community to ask for guidance on how to 
perform these calculations within the Quantum ESPRESSO framework. If 
any of you have experience with this or can point me towards relevant 
resources or documentation, I would greatly appreciate it.


Specifically, I am looking for:

 1. Any tutorials or user guides that cover the calculation of
dielectric constants.
Tips on how to set up my input files for these calculations.
Any example input/output files that could aid my understanding.

I am grateful for any assistance you can provide and am eager to 
contribute back to the community with my findings.


Thank you for your time and help.

Best regards,

Elham Rezaee, PhD student
University of New Brunswick, Canada


___
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--
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IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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and economic cooperation amongst peoples
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Re: [QE-users] Disk space problem: are there ways to instruct QE to NOT print wavefunctions file?

[Lorenzo Paulatto]

Dear Alpin,

pw.x can run without writing the wavefunctions to disk, but ph.x does 
not have this capability. However, if you think that your RAM space is 
sufficient, you can just set outdir to a directory inside /dev/shm, 
which in 99% of modern linux systems is a RAM disk and is user-writeable.


kind regards

On 03/12/2023 08:14, alpin novianus via users wrote:

Dear QE experts,

I had my calculations stopped because my disk space is not enough to 
store the wavefunctions written by QE (ph.x) after the calculation is 
finished.

I am doing electron-phonon = 'lambda_tetra' calculation.

%%
     Error in routine davcio (10):
     error writing file "/_ph0/pwscf.q_9/pwscf.wfc501"
%%

Looking at this error, I realize that in QE, the wavefunction is 
always written to the disk after the calculation.


I am also a VASP user, and in VASP there is an input tag to not write 
the wavefunction (LWAVE).

Is there a similar method to do this in quantum espresso (ph.x)?

It doesn't seem that the wavefunction files will be needed for the 
post-processing (?), so I wonder if they don't need to be written 
actually.

But I may be completely wrong. Please correct me if so.

Thank you for your advice,
Best regards,
Alpin N. Tatan
University of Tokyo

___
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phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
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Re: [QE-users] In Phonon Calculation for Raman Spectra, How to decide to use how many unit cells?

[Lorenzo Paulatto]

Sorry but for 1 more naive question,  if I use 2 unit cell instead of 
1 in DFPT, would it be expected to have difference between the two 
cases ( only at Gamma point) ?


yes, it is different. Because you would get twice as many phonons, but 
half of them would be periodic inside the supercell (and correspond to 
Gamma) the other would not be (and correspond to a zone-border q-point).


hth





Best Regards,

HY Lu





在 2023年11月15日 星期三 下午03:56:04 [GMT+8]， Lorenzo 
Paulatto 寫道：



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On 15/11/2023 08:45, ludwigboltzmann.s...@nycu.edu.tw 
<mailto:ludwigboltzmann.s...@nycu.edu.tw> wrote:
 Hope this will give you an idea why such*symmetry reduced* supercell 
calculation is being carried out.



The idea is "symmetry reduced".

I.e. DFPT allows you to simulate a monochromatic perturbation of any 
periodicity with a unit cell, while frozen phonon can only simulate 
perturbation which have the periodicity of the cell you are using. But 
to break symmetry, you need a supercell.


kind regards

L


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IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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Re: [QE-users] In Phonon Calculation for Raman Spectra, How to decide to use how many unit cells?

[Lorenzo Paulatto]

On 15/11/2023 08:45, ludwigboltzmann.s...@nycu.edu.tw wrote:
 Hope this will give you an idea why such*symmetry reduced* supercell 
calculation is being carried out.



The idea is "symmetry reduced".

I.e. DFPT allows you to simulate a monochromatic perturbation of any 
periodicity with a unit cell, while frozen phonon can only simulate 
perturbation which have the periodicity of the cell you are using. But 
to break symmetry, you need a supercell.


kind regards

L
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Re: [QE-users] ph.x Not writing all the dynamical matrices files

[Lorenzo Paulatto]

The electric field response calculation did not converge. This typically 
indicates a problem with your system (i.e. a metal treated like an 
insulator).


kind regards



On 10/31/23 13:16, Eesha Sanjay Andharia wrote:

Hi Lorenzo,
   Sorry about that. PFA the output files.

Best,
Eesha

*From:* users  on behalf of 
Lorenzo Paulatto 

*Sent:* Tuesday, October 31, 2023 6:10 AM
*To:* users@lists.quantum-espresso.org 
*Subject:* Re: [QE-users] ph.x Not writing all the dynamical matrices 
files


Dear Eesha,

you should provide the output as well, because nobody is going to 
spend 15 minutes to rerun your calculations just to find out what is 
going on.


kind regards


On 10/31/23 10:58, Eesha Sanjay Andharia wrote:

Hi everyone,
   I tried using ph.x with ldisp = true for calculating phonon 
dispersion relations. See attached along with pwscf.in file.
However, it only writes dyn0 -a list of q-points and does not 
calculate the dynamical matrices at those q-points. I tried running 
using different versions and different clusters as well, however, the 
output is the same. No .dyn files.


Is there something wrong with my scf calculations? I cannot pinpoint 
anything specific.
Or do we need to do gamma point and q not equal to 0 calculations 
before using ldisp = true?

Please help.

Thanks!
Eesha

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phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ 
<http://www.impmc.upmc.fr/~paulatto/> - https://anharmonic.github.io/ 
<https://anharmonic.github.io/>

23-24/423 B115, 4 place Jussieu 75252 Paris CX 05

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phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
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Re: [QE-users] ph.x Not writing all the dynamical matrices files

[Lorenzo Paulatto]

Dear Eesha,

you should provide the output as well, because nobody is going to spend 
15 minutes to rerun your calculations just to find out what is going on.


kind regards


On 10/31/23 10:58, Eesha Sanjay Andharia wrote:

Hi everyone,
   I tried using ph.x with ldisp = true for calculating phonon 
dispersion relations. See attached along with pwscf.in file.
However, it only writes dyn0 -a list of q-points and does not 
calculate the dynamical matrices at those q-points. I tried running 
using different versions and different clusters as well, however, the 
output is the same. No .dyn files.


Is there something wrong with my scf calculations? I cannot pinpoint 
anything specific.
Or do we need to do gamma point and q not equal to 0 calculations 
before using ldisp = true?

Please help.

Thanks!
Eesha

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Re: [QE-users] about making two core hole pseudopotentials

[Lorenzo Paulatto]

DearTakahisa,

This file cannot generate the output you claim, there is a syntax error 
that would kick in much sooner.


lpaw=.fales.,

Anyway, the best way to understand a pseudopotential is to plot the 
wavefunctions (all-electron, norm-conserving, ultrasoft) and see where 
you are cutting. If it is too close to a node, disaster will often ensue.


kind regards

On 31/10/2023 07:47, Ishiyama,Takahisa_石山 貴久 wrote:


Dear all,

I’m trying to produce the pseudopotential with two core hole using ld1.x.

But error occurs and stops.

Input and output are attached.

%%

 task # 0

 from compute_phius : error # 1

 problems with find_qi

%%

What is wrong in making the pseudopotential ?

Thank you,

Takahisa Ishiyama


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Re: [QE-users] REGARDING ERROR IN HSE CALCULATION

[Lorenzo Paulatto]

Extrapolation is not interpolation.

kind regards

On 14/10/2023 12:48, Priyanka A J, Res. Associate, Dept. of Physics, IIT 
(BHU) via users wrote:

Dear Quantum espresso users
I am getting this error in hse calculations
"ask #         1
     from  read_namelists : error #         1
      bad line in namelist : "  x_gamma_interpolation = .true." 
(error could be in the previous line)"

My input file is:

  calculation = 'scf'
  etot_conv_thr =   8.00d-05
  forc_conv_thr =   1.00d-04
  outdir = './out/'
  prefix = 'aiida'
  pseudo_dir = './pseudo/'
  tprnfor = .true.
  tstress = .true.
  verbosity = 'high'
/

  degauss =   1.4699723600d-02
  ecutrho =   7.20d+02
  ecutwfc =   9.00d+01
    ibrav       = 0
    nat         = 40
    ntyp        = 3
    nspin = 2
    nbnd = 140
    input_dft = 'hse'
    nqx1 = 1, nqx2 = 1, nqx3 = 1
    x_gamma_interpolation = .true.
    exxdiv_treatment = 'gygi-baldereschi'
    nosym = .true., noinv = .true
  starting_magnetization(1) =   1.00d-01
  starting_magnetization(2) =   1.00d-01
  starting_magnetization(3) =   1.00d-01
/


  conv_thr =   1.00d-05
  mixing_beta =   4.00d-01
  diagonalization = 'cg'
/

K_POINTS automatic
3 3 3 0 0 0
ATOMIC_SPECIES
Sn    118.71000  sn_pbesol_v1.4.uspp.F.UPF
Cs    132.90545  cs_pbesol_v1.uspp.F.UPF
I     126.90447  I.pbesol-n-kjpaw_psl.0.2.UPF

ATOMIC_POSITIONS {angstrom}
Sn      6.142741   6.142741   6.142741
Sn      0.00   6.142741   0.00
Sn      6.142741   0.00   0.00
Sn      0.00   0.00   6.142741
Cs      0.00   0.00   0.00
Cs      6.142741   0.00   6.142741
Cs      0.00   6.142741   6.142741
Cs      6.142741   6.142741   0.00
I      11.598723   5.698252   2.949007
I       0.686758   6.587229   9.336474
I       6.829499   6.587229   9.091747
I       5.455982   5.698252   3.193734
I       0.686758  11.840992   3.193734
I      11.598723   0.89   9.091747
I       5.455982   0.89   9.336474
I       6.829499  11.840992   2.949007
I       2.949007  11.598723   5.698252
I       9.336474   0.686758   6.587229
I       9.091747   6.829499   6.587229
I       3.193734   5.455982   5.698252
I       3.193734   0.686758  11.840992
I       9.091747  11.598723   0.89
I       9.336474   5.455982   0.89
I       2.949007   6.829499  11.840992
I       5.698252   2.949007  11.598723
I       6.587229   9.336474   0.686758
I       6.587229   9.091747   6.829499
I       5.698252   3.193734   5.455982
I      11.840992   3.193734   0.686758
I       0.89   9.091747  11.598723
I       0.89   9.336474   5.455982
I      11.840992   2.949007   6.829499
I       2.984021   2.984021   2.984021
I       9.301461   9.301461   9.301461
I       3.158720   9.301461   9.126761
I       9.126761   2.984021   3.158720
I       9.301461   9.126761   3.158720
I       2.984021   3.158720   9.126761
I       9.126761   3.158720   9.301461
I       3.158720   9.126761   2.984021

CELL_PARAMETERS angstrom
      12.28550       0.00       0.00
      0.00       12.28550       0.00
      0.0        0.00       12.28550
EOF
Regards
Priyanka

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Re: [QE-users] Error in Hubbard calculations

[Lorenzo Paulatto]

HUBBARD {ortho-atomic}

U Sn-2p 0.5



I guess you should target 5p orbitals, not 2p. Nomenclature can vary 
between files (and different codes used to generate them), but you can 
always check in the UPF files what the valence orbitals have been called.


hth




Regards
Priyanka

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[QE-users] Fwd: Missing d orbital in projected band structure of CaC6

[Lorenzo Paulatto]

 Forwarded Message 
Subject: 	Re: [QE-users] Missing d orbital in projected band structure 
of CaC6

Date:   Tue, 25 Jul 2023 10:15:26 +0200
From:   Lorenzo Paulatto 
Organization:   CNRS
To: Bruce Wang 



Hello Bruce.


You can see in hte input file (which is at the beginning of the UPF 
file) that the 3d orbital occupancy has been set to "-1". This mean that 
the name is reserved for later use, but the orbital has not actually 
been computed. Later on, two arbitrary energies (0.05Ry and 1Ry) have 
been defined to construct two reference scattering states for the "d" 
orbitals. These states cannot be used for projecting because they are 
not normalizable.



You can try to set 3d0 and pass the input to ld1:

  ld1.x < input

But if the 3d state is unbound, this will not converge. In that case the 
only solution, is to use a slightly excited configuration, i.e.e take 
away some charge from 4s2 and put it in 3d, but I cannot guarantee that 
the resulting pseudopotential will be accurate.



hth

 
   title='Ca',
   zed=20.,
   rel=1,
config='[Ar] 4s2 4p0 3d-1', iswitch=3,
   dft='PBE'
 /
 
   lpaw=.false.,
   use_xsd=.FALSE.,
   pseudotype=3,
   file_pseudopw='Ca.pbe-spn-rrkjus_psl.1.0.0.UPF',
   author='ADC',
   lloc=-1,
   rcloc=1.5,
   which_augfun='PSQ',
   rmatch_augfun_nc=.true.,
   nlcc=.true.,
   new_core_ps=.true.,
   rcore=1.0,
   tm=.true.
 /
6
3S  1  0  2.00  0.00  1.20  1.30  0.0
4S  2  0  2.00  0.00  1.20  1.30  0.0
3P  2  1  6.00  0.00  1.40  1.60  0.0
4P  3  1  0.00  0.00  1.40  1.60  0.0
3D  3  2  0.000.05   1.20  1.70  0.0
3D  3  2  0.001.00   1.20  1.70  0.0



On 7/25/23 09:40, Bruce Wang wrote:

Dear QE users and developers,

I am currently working on calculating the projected band structure of 
CaC6 using quantum espresso with GGA+UItrasoft pseudopotential 
(Ca.pbe-spn-rrkjus_psl.1.0.0.UPF). However, I have encountered an 
issue with obtaining the 3d orbital wavefunctions for Calcium.


I followed the QE PP examples, and I have managed to obtain the 4s and 
3p orbitals. The 3d orbital was missing while it should existed.


I would greatly appreciate any guidance on how to retrieve the 3d 
orbital character of Calcium for my projected band structure 
calculations.


Thank you for your time and assistance.


Regards,
Bruce

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Re: [QE-users] Quantum Espresso v7.2 installation

[Lorenzo Paulatto]

Yes you can

kind regards

On 19/07/2023 19:19, gang.y...@xju.edu.cn wrote:


Dear all:

Can I install the newest version (Quantum Espresso v7.2) in a linux 
ubuntu 20.04 LTS system?


I saw a example in the website 
https://pranabdas.github.io/espresso/setup/install/. It shows that 
Quantum Espresso 7.2 installed in a Ubuntu (LTS 22.04) system. ​


Thank you!


Gang

07/19/2023


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Re: [QE-users] R: Assistance with the Installation of Quantum Espresso on Ubuntu

[Lorenzo Paulatto]

On 05/07/2023 12:19, Pietro Davide Delugas wrote:

And then compile everything with

make all


I would just start with

make pw pp


"all" takes a lot of time and compiles a lot of stuff that is quite 
specialized, and you will probably not need to begin with.


cheers




--

Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
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Re: [QE-users] A question on the volume_factor flag in d3_tk.x

[Lorenzo Paulatto]

On 6/15/23 21:12, Elio Physics wrote:

Dear professor Paulatto,

Thanks for the information.

1)Would that divergence produce negative line widths? I have been 
trying to obtain some decent results for graphene but when the 
smearing is above 1.0 , the code crashes stating that the linewidth is 
negative! i tried to increase the grid dimension but in vain.



To get a negative linewidth it takes a seriously broken calculation, as 
the last therm can mathematically be negative



But that would require that the population of the higher phonon (q'') is 
higher than the lower phonon (q') as w'' = w+w' > w'.



Also a broken compilation of the code, or a bug, but to say anything I 
would need a specific case to test and reproduce.





2) Is there a flag in the input that ensures regularization or one 
that imposes a cutoff?



No, it has been done ad-hoc for the specific paper about 2D systems, 
although I did not do those calculations, I'm not sure of the details. 
It is very easily done in post-processing, if store_lw=.true. is used to 
save the linewidths to file, using the matlab script recompute_sma.m, or 
any home-made script. A bit more complicated in the exact minimization 
method, setting a reasonable Casimir scattering length may be the best 
bet. Exact algorithm is very expensive to converge anyway, because one 
cannot use shifted grid (and symmetry is not exploited at the moment)







Thank you

*From:* users  on behalf of 
Lorenzo Paulatto 

*Sent:* Thursday, June 15, 2023 5:02 PM
*To:* Quantum ESPRESSO users Forum 
*Subject:* Re: [QE-users] A question on the volume_factor flag in d3_tk.x
Hello Elio,
The problem is that tk is given for bulk per unit of volume. When you 
do a 2D material in plane waves, you need to put a lot of vacuum. The 
volume factor is used to make the value independent on the amount of 
vacuum. It can  is the ratio of the bulk uni cell to the 2d unit cell, 
or the ratio between the c axis in bulk and in the film, it is the 
same thing.


Please not that 2d materials are very tricky: the thermal conductivity 
from the quadratic band is integrable but diverging. Using some kind 
of regularization or a cutoff may be required.


Cheets



On June 15, 2023 8:48:16 p.m. GMT+02:00, Elio Physics 
 wrote:


Dear all (and specifically Professor Paulatto),

Sorry to bother you again with another question regarding the d3q
code. To calculate the lattice thermal conductivity for 2D
materials, we need to define a volume_factor =H/V. H is defined as
the interlayer distance for the corresponding bulk material. If I
understood correctly, let us say we have a 1H MoS2, we know that
the bulk can be modeled as two layers (a total of six atoms per
unit cell). H would then be the distance between the upper S layer
of the bottom MoS2 and the lower S layer of the MoS2 on top. Correct?


Now what if we have a 1T 2D structure. Up to my knowledge, the
bulk is modeled as one layer ( 3 atoms per unit cell).  In this
case, what would H be ? The thickness of the structure?



Regards

Elie Moujaes
Federal University of Rondonia
Brazil
Porto Velho


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Re: [QE-users] A question on the volume_factor flag in d3_tk.x

[Lorenzo Paulatto]

Hello Elio,
The problem is that tk is given for bulk per unit of volume. When you do a 2D 
material in plane waves, you need to put a lot of vacuum. The volume factor is 
used to make the value independent on the amount of vacuum. It can  is the 
ratio of the bulk uni cell to the 2d unit cell, or the ratio between the c axis 
in bulk and in the film, it is the same thing.

Please not that 2d materials are very tricky: the thermal conductivity from the 
quadratic band is integrable but diverging. Using some kind of regularization 
or a cutoff may be required.

Cheets



On June 15, 2023 8:48:16 p.m. GMT+02:00, Elio Physics  
wrote:
>Dear all (and specifically Professor Paulatto),
>
>Sorry to bother you again with another question regarding the d3q code. To 
>calculate the lattice thermal conductivity for 2D materials, we need to define 
>a volume_factor =H/V. H is defined as the interlayer distance for the 
>corresponding bulk material. If I understood correctly, let us say we have a 
>1H MoS2, we know that the bulk can be modeled as two layers (a  total of six 
>atoms per unit cell). H would then be the distance between the upper S layer 
>of the bottom MoS2 and the lower S layer of the MoS2 on top. Correct?
>
>
>Now what if we have a 1T 2D structure. Up to my knowledge, the bulk is modeled 
>as one layer ( 3 atoms per unit cell).  In this case, what would H be ? The 
>thickness of the structure?
>
>
>
>Regards
>
>Elie Moujaes
>Federal University of Rondonia
>Brazil
>Porto Velho
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Re: [QE-users] [D3q-discuss] Error executing d3_q2r.x

[Lorenzo Paulatto]

Thanks for the advice.  The idea was to run it on one processor with 
no OPENMPTHREADS since it is a postprocessing calculation.
I was able to resolve the d3_q2r.x problem. The solution was to 
substitute '<' by '-in'. Everything goes well.

I still have to figure out the 'NaN' in the ASR output file.



Hello Elio,

try to run the asr3 code without OMP threads either, it is supported in 
principle but not very tested. As you get NaN from the beginning, it 
could be some corner case I did not think of, i.e. all terms are zero 
(this happens for example in 2x2x2 cell for crystals of some specific 
symmetries, like GeTe). If you wish, you can send me the  anharmonic 
matrix files and I can have a look directly.


regards




On the other hand, I am trying to get the phonon dispersion & group 
velocities by calling the d3_r2q routine. I used the following input:



calculation='freq'
prefix='si'
outdir='/scratch/90022a/eamouj78/si'
file_mat2='mat2R'
asr2='simple'
nq=5
print_velocity=.true.
/
QPOINTS crystal
0.50 0.50 0.50
0.00 0.00 0.00 70
0.50 0.00 0.5 70
0.50 0.25 0.75 70
0.00 0.00 0.00 70

The code crashes with a mysterious error:

%% 


     Error in routine start_nanoclock (1):
     rigid block clock is already running
 %%

Prof. Pauletto, is there anything wrong with the above input? I could 
not find any input example on this one


Regards




*From:* Paolo Giannozzi 
*Sent:* Friday, June 9, 2023 11:37 AM
*To:* Elio Physics 
*Cc:* Quantum ESPRESSO users Forum 
*Subject:* Re: [QE-users] [D3q-discuss] Error executing d3_q2r.x
Unrelated: you should not run so many OpenMP threads (48), it is very
inefficient.

Paolo

On 6/9/23 13:49, Elio Physics wrote:
> Dear prof. Paulatto,
>
> Thanks for your quick response. This is weird. I am using the correct
> d3_q2r.x executable. I have taken a screen shot of the error (I have
> attached it to this e-mail).
> I am also getting a weird result when I call the d3_asr.x 
executable.  I

> am getting a lot of "NaN" with no values in the output file (also
> attached a screenshot of the output file).
>
>
> Thank you for your help
>
> Regards
> ----
> *From:* Lorenzo Paulatto 
> *Sent:* Friday, June 9, 2023 5:09 AM
> *To:* d3q-disc...@lists.sourceforge.net 


> *Subject:* Re: [D3q-discuss] Error executing d3_q2r.x
>
> Hello Elio,
>
> I copy-pasted your input and it works for me.
>
> The error must be elsewhere (are you sure you're not calli d3_r2q.x
> instead?)
>
> kind regards
>
>
>
> On 6/9/23 03:59, Elio Physics wrote:
>> Dear  all,
>>
>> I am trying to test the d3q code by reproducing the results for
>> Silicon. Everything went fine except when I execute the d3_q2r.x flag
>> which applies to the 2^nd order dynamical matrices.  The dynamical
>> matrices for the 8 points in the q grid were produced as "matdyn0",
>> "matdyn1", "matdyn2",,"matdyn8". My d3_q2r.x input is:
>>
>> 
>> fildyn  =  'matdyn'
>> flfrc   =  'mat2R'
>>  /
>>
>> However the code crashes with the error:
>>
>> 
 %%

>>      Error in routine q2r (1):
>>      error reading input namelist
>> 
 %%

>>
>> I cannot figure out what is wrong with the input. I tried to rename
>> the files as "dyn0", "dyn1", and set fildyn='dyn', but I still get
>> the same error. Can anyone spot what the error could be?
>>
>> Thanks in advance..
>>
>> Elie Albert Moujaes
>> Adjunct professor level 4
>> Federal University of Rondonia
>> Brazil
>>
>>
>> ___
>> D3q-discuss mailing list
>> d3q-disc...@lists.sourceforge.net  
<mailto:d3q-disc...@lists.sourceforge.net 
<mailto:d3q-disc...@lists.sourceforge.net>>
>> https://lists.sourceforge.net/lists/listinfo/d3q-discuss 
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Fd3q-discuss=05%7C01%7Cpaolo.giannozzi%40uniud.it%7C21627b1f996149a824b108db68dfbd9e%7C6e6ade15296c4224ac581c8ec2fd53a8%7C0%7C0%7C638219082413150526%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C=XDWx6auOZRyTtvb4fgxWxOar%2F5AtqAEcRywaHEgmfkU%3D=0 
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Re: [QE-users] [SPAM] Calculation of static dielectric tensor

[Lorenzo Paulatto]

The static dielectric matrix is computed by the phonon (ph.x) code, with option 
epsil=.true., you can set trans=.false. if you want to avoid computing also the 
phonons.

The epsil.x code computes the dynamical dielectric matrix (with a sum over 
empty states if I remember correctly). It should match the other in the low 
energy limit.

Hth

On June 2, 2023 10:01:45 p.m. GMT+02:00, "Филанович Антон" 
 wrote:
>___
>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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>users mailing list users@lists.quantum-espresso.org
>https://lists.quantum-espresso.org/mailman/listinfo/users___
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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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Re: [QE-users] [EXTERNAL] The phonon code with Raman and Hubbard U is not implemented

[Lorenzo Paulatto]

p.s. to convert from 1/bohr² to 1/Ų you just have to multiply by 
(1/0.529...)²



On 5/12/23 10:05, Lorenzo Paulatto wrote:

On 5/11/23 22:33, Karkee, Rijan wrote:


Hi Lorenzo,


I saw your tutorial and input files. So it produces Raman tensor for 
each displaced atom so if there are 10 atoms then I have to generate 
for all.



Quick question,   for each atom I see there are three different 
tensor. How  can we generate the other two?




The Raman tensor has dimension 3x3x(3*nat), it corresponds to deriving 
teh dielectric matrix (3x3) with respect to the displacement of each 
atom (nat) along eahc cartesian direction (3), or equivalently along 
each phonon polarization (3*nat, but then you need to rotate it to 
cartesian coordinates).



In the example, I only derive epsilon w.r.t. the first atom along 
direction x. Because Silicon is so symmetric, all the other components 
of the tensor look are identical but rotated. This is not true in 
general, however, if the system has symmetry, it is always possible to 
use it to reduce the amount of computation, but it takes some human 
time, at least once, to write a code that does it.


hth



The magnitude looks same but seems rotated by some matrix. And how 
does one converts au^-1 in cartesian axis to A^2? For example in 
below, 2.524312370 has been converted into 0.166309336301E+02 but I 
could not understand the conversion.





    Raman tensor (au^-1) in cartesian axis

   atom  1
  (   0.0   0.0 0.0 )
  (   0.0   0.0 2.524312370 )
  (   0.0   2.524312370 0.0 )

  (   0.0   0.0 2.524312370 )
  (  -0.0  -0.0 -0.0 )
  (   2.524312370   0.0 -0.0 )

  (   0.0   2.524312370 0.0 )
  (   2.524312370   0.0 -0.0 )
  (   0.0  -0.0 0.0 )

   atom  2
  (   0.0  -0.0 -0.0 )
  (  -0.0  -0.0 -2.493208807 )
  (  -0.0  -2.493208807 -0.0 )

  (  -0.0  -0.0 -2.493208807 )
  (  -0.0  -0.0 0.0 )
  (  -2.493208807   0.0 -0.0 )

  (   0.0  -2.493208807 -0.0 )
  (  -2.493208807   0.0 0.0 )
  (  -0.0  -0.0 -0.0 )


 Raman tensor (A^2)

 atom #    1    pol.  1
  0.603445027917E-14  0.566872601983E-14 0.896024435392E-14
  0.347438046377E-14  0.603445027917E-14 0.166309336301E+02
  0.182862129672E-15  0.166309336301E+02 0.603445027917E-14
 atom #    1    pol.  2
  0.128003490770E-14  0.182862129672E-15 0.166309336301E+02
 -0.548586389016E-15 -0.182862129672E-15 -0.274293194508E-14
  0.166309336301E+02  0.603445027917E-14 -0.148118325034E-13
 atom #    1    pol.  3
  0.603445027917E-14  0.166309336301E+02 0.603445027917E-14
  0.166309336301E+02  0.603445027917E-14 -0.182862129672E-15
  0.310865620442E-14 -0.603445027917E-14 0.896024435392E-14


*From:* users  on behalf of 
Lorenzo Paulatto 

*Sent:* Thursday, May 11, 2023 12:55:32 PM
*To:* users@lists.quantum-espresso.org
*Subject:* Re: [QE-users] [EXTERNAL] The phonon code with Raman and 
Hubbard U is not implemented



On 11/05/2023 17:28, Lorenzo Bastonero wrote:

Dear Rijan,

To warn you: these steps are involved, and you might need to code 
quite a bit and have to know the theory behind. Refer to the before 
mentioned paper.



There is a half-way solution, which consists in doing numerical 
derivatives of the dielectric constants. This works with LDA+U with 
"Atomic" type projections, but not LDA+U+V.


I did a tutorial (very simplified) a few years ago, it shoudl be here:

https://drive.google.com/drive/folders/0Bzgwv8VZEl9SRDQwckRJVlkyUzA?resourcekey=0-BnSQk84YUeRvCNze9XKCAA=sharing

hth




If you are willing to do so, you can find the first steps in example 
10 of PW 
(https://gitlab.com/QEF/q-e/-/tree/develop/PW/examples/example10).


Then you might try to have a look in the PHonon/FD module 
(https://gitlab.com/QEF/q-e/-/tree/develop/PHonon/FD).


All the best,
Lorenzo


Lorenzo Bastonero

PhD Student
U Bremen Excellence Chair,
Bremen Center for Computational Materials Science,
and MAPEX Center for Materials and Processes

University of Bremen
Faculty of Production Engineering
TAB-Building, Room 3.32
Am Fallturm 1
28359 Bremen, DE

http://www.hmi.uni-bremen.de/

Il giorno 11 mag 2023, alle ore 16:13, Karkee, Rijan 
 ha scritto:


Hi Lorenzo,

Thanks for the information. 

Re: [QE-users] [EXTERNAL] The phonon code with Raman and Hubbard U is not implemented

[Lorenzo Paulatto]

On 5/11/23 22:33, Karkee, Rijan wrote:


Hi Lorenzo,


I saw your tutorial and input files. So it produces Raman tensor for 
each displaced atom so if there are 10 atoms then I have to generate 
for all.



Quick question,   for each atom I see there are three different 
tensor. How  can we generate the other two?




The Raman tensor has dimension 3x3x(3*nat), it corresponds to deriving 
teh dielectric matrix (3x3) with respect to the displacement of each 
atom (nat) along eahc cartesian direction (3), or equivalently along 
each phonon polarization (3*nat, but then you need to rotate it to 
cartesian coordinates).



In the example, I only derive epsilon w.r.t. the first atom along 
direction x. Because Silicon is so symmetric, all the other components 
of the tensor look are identical but rotated. This is not true in 
general, however, if the system has symmetry, it is always possible to 
use it to reduce the amount of computation, but it takes some human 
time, at least once, to write a code that does it.


hth



The magnitude looks same but seems rotated by some matrix. And how 
does one converts au^-1 in cartesian axis to A^2? For example in 
below, 2.524312370 has been converted into 0.166309336301E+02 but I 
could not understand the conversion.





    Raman tensor (au^-1) in cartesian axis

   atom  1
  (   0.0   0.0 0.0 )
  (   0.0   0.0 2.524312370 )
  (   0.0   2.524312370 0.0 )

  (   0.0   0.0 2.524312370 )
  (  -0.0  -0.0 -0.0 )
  (   2.524312370   0.0 -0.0 )

  (   0.0   2.524312370 0.0 )
  (   2.524312370   0.0 -0.0 )
  (   0.0  -0.0 0.0 )

   atom  2
  (   0.0  -0.0 -0.0 )
  (  -0.0  -0.0 -2.493208807 )
  (  -0.0  -2.493208807 -0.0 )

  (  -0.0  -0.0 -2.493208807 )
  (  -0.0  -0.0 0.0 )
  (  -2.493208807   0.0 -0.0 )

  (   0.0  -2.493208807 -0.0 )
  (  -2.493208807   0.0 0.0 )
  (  -0.0  -0.0 -0.0 )


 Raman tensor (A^2)

 atom #    1    pol.  1
  0.603445027917E-14  0.566872601983E-14 0.896024435392E-14
  0.347438046377E-14  0.603445027917E-14 0.166309336301E+02
  0.182862129672E-15  0.166309336301E+02 0.603445027917E-14
 atom #    1    pol.  2
  0.128003490770E-14  0.182862129672E-15 0.166309336301E+02
 -0.548586389016E-15 -0.182862129672E-15 -0.274293194508E-14
  0.166309336301E+02  0.603445027917E-14 -0.148118325034E-13
 atom #    1    pol.  3
  0.603445027917E-14  0.166309336301E+02 0.603445027917E-14
  0.166309336301E+02  0.603445027917E-14 -0.182862129672E-15
  0.310865620442E-14 -0.603445027917E-14 0.896024435392E-14


*From:* users  on behalf of 
Lorenzo Paulatto 

*Sent:* Thursday, May 11, 2023 12:55:32 PM
*To:* users@lists.quantum-espresso.org
*Subject:* Re: [QE-users] [EXTERNAL] The phonon code with Raman and 
Hubbard U is not implemented



On 11/05/2023 17:28, Lorenzo Bastonero wrote:

Dear Rijan,

To warn you: these steps are involved, and you might need to code 
quite a bit and have to know the theory behind. Refer to the before 
mentioned paper.



There is a half-way solution, which consists in doing numerical 
derivatives of the dielectric constants. This works with LDA+U with 
"Atomic" type projections, but not LDA+U+V.


I did a tutorial (very simplified) a few years ago, it shoudl be here:

https://drive.google.com/drive/folders/0Bzgwv8VZEl9SRDQwckRJVlkyUzA?resourcekey=0-BnSQk84YUeRvCNze9XKCAA=sharing

hth




If you are willing to do so, you can find the first steps in example 
10 of PW 
(https://gitlab.com/QEF/q-e/-/tree/develop/PW/examples/example10).


Then you might try to have a look in the PHonon/FD module 
(https://gitlab.com/QEF/q-e/-/tree/develop/PHonon/FD).


All the best,
Lorenzo


Lorenzo Bastonero

PhD Student
U Bremen Excellence Chair,
Bremen Center for Computational Materials Science,
and MAPEX Center for Materials and Processes

University of Bremen
Faculty of Production Engineering
TAB-Building, Room 3.32
Am Fallturm 1
28359 Bremen, DE

http://www.hmi.uni-bremen.de/

Il giorno 11 mag 2023, alle ore 16:13, Karkee, Rijan 
 ha scritto:


Hi Lorenzo,

Thanks for the information. May I know, for now, what steps are 
involved so that I can compute those steps by hand?
I want to know which module to run first and 

Re: [QE-users] [EXTERNAL] The phonon code with Raman and Hubbard U is not implemented

[Lorenzo Paulatto]

onomic cooperation amongst peoples
___
Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
users mailing listus...@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

--
Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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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users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] [Spam:]Re: About the calculation of dielectric function by using QE package

[Lorenzo Paulatto]

as for the NCPP there are numerous PP for different elements, for instance, I 
often use the ONCVPSP  (Optimized Norm-Conservinng Vanderbilt PSeudopotential) 
by D. R. Hamann (Phys. Rev. B 88, 085117 (2013)) which can be found 
onhttp://quantum-simulation.org/potentials/sg15_oncv/.


Just a little precision: there is a confusion between ONCV and SG15. The 
pseudopotentials you linked are the SG15 library (M. Schlipf and F. 
Gygi, Computer Physics Communications 196, 36 (2015)), they have been 
generated using the ONCV code by Hamann ( D. R. Hamann, Phys. Rev. B 88, 
085117 (2013)). Another library that uses the same code is the 
Pseudo-DOJO one.


Also, as we are in topic, there is a vast collection of norm-conserving 
pseudoopotentials in the pslibrary of Andrea Dal Corso, and you can find 
"old" norm-conserving library such as the FHI and BHS ones by exploring 
the website.


hth





Best,
Simon

Am Dienstag, April 11, 2023 14:39 CEST, schrieb PURINUT 
SAE-FU:


Hello

I'm trying to calculate the dielectric functions of the materials. By searching 
on the internet, the dielectric functions can be calculated by using the 
epsilon.x code in the QE package. However, I found that there is a limitation 
that requires only norm-conserving pseudopotential (NCPP). I look into the 
pseudopotential library on these 2 websites,

1)http://pseudopotentials.quantum-espresso.org/legacy_tables

2)https://www.materialscloud.org/discover/sssp/table/efficiency

but I cannot find the NCPP files. I would like to ask 1) Where can I get the 
NCPP files? 2) Is there a way to calculate the dielectric function of the 
material that applied PAW pseudopotential?

Best regards,

PURINUT SAE-FU
Ph.D. Student
Department of Physics, Faculty of Science, Mahidol University, Thailand


___
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people and expresses its concerns about the devastating
effects that the Russian military offensive has on their
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--
Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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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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users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] Phonon calculations

[Lorenzo Paulatto]

Yes.
If you still have the dynamical matrix files, just make a copy of them, then 
open the first one with a text editor, there is a line with a single T in it. 
Change it to an F. Then remove the following few lines which contain the static 
dielectric matrix and effective charges. Save the file and redo q2r and matdyn.

If you do not have the files, you cane reconstruct then with matdyn and q2qstar.

hth

On April 9, 2023 8:59:38 p.m. GMT+02:00, BOUAFIA HAMZA 
 wrote:
>Hi,
>is it possible to disable LOTO splitting without redoing the phonon 
>calculation ?(restart from an existing LOTO calculations)
>Sincerely
>
___
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Re: [QE-users] Problem installing QE in Windows 11 using Kali Linux

[Lorenzo Paulatto]

Kali linux is a distribution specialized for network penetration testing, I 
highly doubt that it is suitable for compiling scientific code. Granted that 
all distributions are the same after you have installed the right package, I 
would recommend you start from a general purpose one.

Kind regards 



On March 27, 2023 8:07:27 p.m. GMT+02:00, "Dumre, Bishal Babu B" 
 wrote:
>Hello there,
>
>I am trying to install quantum espresso inside Windows 11. I am using Kali 
>linux distribution. I tried using many other distributions but Kali linux was 
>better than others. After installing dependencies like git and Fortran, I was 
>able to run "./configure" command, but, finally the "make all" command does 
>not work. I tried many variations of make all command, but it does not work. 
>The details of error is given below:
>
>
>$ make all
>test -d bin || mkdir bin
>cd install ; make -f extlibs_makefile libfox
>make[1]: Entering directory '/mnt/c/Users/Bishal 
>Dumre/Desktop/QuantumEspresso/qe-7.1/install'
>if test ! -d ../FoX ; then \
>  cd /mnt/c/Users/ Dumre/Desktop/QuantumEspresso/qe-7.1//external/fox; \
>./configure --prefix=/mnt/c/Users/ 
> Dumre/Desktop/QuantumEspresso/qe-7.1//FoX FC=gfortran FCFLAGS=""; \
>touch cp_test; \
>if cp -p cp_test cp_test_1; then \
>rm cp_test_1; \
>echo "cp -p works"; \
>else \
>find -type f | xargs sed -i 's/cp -p/cp/g'; \
>fi; \
>rm cp_test; \
>make install && make clean; \
> cd -; \
>fi
>/bin/sh: 3: ./configure: not found
>touch: cannot touch 'cp_test': Permission denied
>cp: cannot stat 'cp_test': No such file or directory
>sed: can't read ./Bishal: No such file or directory
>sed: can't read Dumre/.burai/.properties: No such file or directory
>sed: can't read ./Bishal: No such file or directory
>sed: can't read Dumre/.burai/.pseudopot/.pseudolist: N
>.
>.
>.
>.
>Trailing errors of sed: A lot.
>.
>.
>.
>.
>sed: can't read Framework/Obligations/CND2023R23.xml: No such file or directory
>sed: can't read ./Default/AppData/Local/Microsoft/Internet: No such file or 
>directory
>sed: can't read Explorer/MSIMGSIZ.DAT: No such file or directory
>sed: couldn't open temporary file 
>./Default/AppData/Local/Microsoft/Windows/INetCache/IE/sedoEwhLu: Permission 
>denied
>rm: cannot remove 'cp_test': No such file or directory
>make[2]: Entering directory '/mnt/c/Users'
>make[2]: *** No rule to make target 'install'.  Stop.
>make[2]: Leaving directory '/mnt/c/Users'
>/mnt/c/Users/Bishal Dumre/Desktop/QuantumEspresso/qe-7.1/install
>make[1]: Leaving directory '/mnt/c/Users/Bishal 
>Dumre/Desktop/QuantumEspresso/qe-7.1/install'
>( cd UtilXlib ; make TLDEPS= all || exit 1 )
>make[1]: Entering directory '/mnt/c/Users/Bishal 
>Dumre/Desktop/QuantumEspresso/qe-7.1/UtilXlib'
>Makefile:49: make.depend: No such file or directory
>make[1]: *** No rule to make target 'make.depend'.  Stop.
>make[1]: Leaving directory '/mnt/c/Users/Bishal 
>Dumre/Desktop/QuantumEspresso/qe-7.1/UtilXlib'
>make: *** [Makefile:209: libutil] Error 1
>
>
>Please help me.
>
>Yours,
>Bishal Dumre
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Re: [QE-users] Compilation Issue

[Lorenzo Paulatto]

/usr/bin/ld: cannot find -lmpi_usempif08


Hello Vinky,

normally you do not link fortran code with ld, but with the fortran 
compiler itself, which should be the default unless you tamper with the 
./configure parameters. If you want more help, please provide more 
detail about what you are doing (i.e.e every command you type to arrive 
at the error and teh entire configure output)



make[2]: Leaving directory 
'/home/student/qe-7.1-ReleasePack/qe-7.1/PW/src'


At your institute, students do not have the right to a name?

cheers




make[1]: *** [Makefile:9: pw] Error 1
make[1]: Leaving directory '/home/student/qe-7.1-ReleasePack/qe-7.1/PW'
make: *** [Makefile:71: pw] Error 1

Could anyone help solving this?
Thank you!

Regards,
Vinky

___
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--
Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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Re: [QE-users] users Digest, Vol 187, Issue 14(unsubscribe)

[Lorenzo Paulatto]

On March 19, 2023 3:43:46 p.m. GMT+01:00, ogunku...@physics.unaab.edu.ng wrote:
>
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>> Today's Topics:
>>
>>1. Re: on-site attraction in DFT+U (Mpayami)
>>2. invalid lattice parameters error (Mr. Sheharyar Pervez RA FES)
>>3. Re: invalid lattice parameters error (Lorenzo Paulatto)
>>4. Re: invalid lattice parameters error (Mr. Sheharyar Pervez RA FES)
>>5. cell_dofree (Mpayami)
>>6. Re: cell_dofree (Mpayami)
>>7. Re: cell_dofree (Mr. Sheharyar Pervez RA FES)
>>8. Re: cell_dofree (Lorenzo Paulatto)
>>9. Re: cell_dofree (Mpayami)
>>   10. Re: cell_dofree (Mpayami)
>>
>>
>> --
>>
>> Message: 1
>> Date: Wed, 15 Feb 2023 14:44:18 +0330
>> From: Mpayami 
>> To: "Iurii TIMROV" ,  "Quantum ESPRESSO users
>>  Forum" 
>> Subject: Re: [QE-users] on-site attraction in DFT+U
>> Message-ID: <0f94cbf0b9c1e44daf5bb71ff3712...@aeoi.org.ir>
>> Content-Type: text/plain; charset="utf-8"
>>
>>
>> Dear Iurii,
>>
>> Hi and thanks.
>>
>> Bests,
>>
>> Mahmoud
>>
>>
>> - Original Message -
>> From: Iurii TIMROV via users (users@lists.quantum-espresso.org)
>> Date: 26/11/1401 13:43
>> To: Mpayami (mpay...@aeoi.org.ir), Quantum ESPRESSO users Forum
>> (users@lists.quantum-espresso.org)
>> Subject: Re: [QE-users] on-site attraction in DFT+U
>>
>>
>>> Is there a philosophy behind this change?
>>
>>
>> No, it was just overlooked, here is the fix:
>> https://gitlab.com/QEF/q-e/-/merge_requests/2035/diffs
>>
>>
>> Iurii
>>
>> --
>> Dr. Iurii TIMROV
>> Senior Research Scientist
>> Theory and Simulation of Materials (THEOS)
>> Swiss Federal Institute of Technology Lausanne (EPFL)
>> CH-1015 Lausanne, Switzerland
>> +41 21 69 34 881
>> http://people.epfl.ch/265334
>>
>> From: users  on behalf of
>> Mpayami via users 
>> Sent: Monday, February 13, 2023 8:20:15 PM
>> To: Quantum ESPRESSO users Forum
>> Subject:[QE-users] on-site attraction in DFT+U
>> ?
>>
>> Dear QE Developers,
>>
>> Hi.
>> I noticed that in QE-6.4.1, it is possible to apply an on-site
>> "attraction" (U<0) for Hubbard correction in DFT+U, but in QE-7.1, the
>> code accepts only on-site "repulsion" (U>0). Is there a philosophy behind
>> this change?
>> Thanks in advance.
>>
>> Best regards,
>>
>>
>> Mahmoud Payami
>> NSTRI, AEOI
>> Tehran, Iran
>> Email: mpay...@aeoi.org.ir
>> Phone: +98(0)2182066504
>> 
>>
>> ___
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>> Message: 2
>> Date: Wed, 15 Feb 2023 14:23:19 +
>> From: "Mr. Sheharyar Pervez RA FES" 
>> To: Quantum ESPRESSO users Forum 
>> Subject: [QE-users] invalid lattice parameters error
>> Message-ID:
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>> Content-T

Re: [QE-users] [SPAM] How to deal with a mode of phonon spectrum that cannot converge

[Lorenzo Paulatto]

On 15/03/2023 07:14, zhouchao via users wrote:
How to deal with a mode of phonon spectrum that cannot converge, how 
to make it converge, tried many methods, but can not be solved。
how to explain this problem, what is the reason, is it a problem of 
the structure itself, how to analyze it?


This output line give a suggestion:

Possibly too few bands at point    1   0.0   0.0   0.0

your scf calculation has been done with 23 electronic bands (Kohn-Sham 
states), but it may not be enough for the phonon caculaiton. Try to 
increase this value a bit in the pw.x input


You can also try to increase nmix_ph, as hinted in the manual, to 20.

Finally, you can and decrease alpha_mix, and add a few more iterations 
of mixing, i.e.


alpha_mix = 0.3, 0.1, 0.05, 0.01


hth



As shown in the end of the attachment, the first 10 modes all 
converge, but the 11th mode fails to converge.


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phone: +33 (0)1 442 79822 / skype: paulatz
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Re: [QE-users] Fwd: Hydrogen atom pseudopotential files with q=1.5e and q=0.75e (PBE, USPP)

[Lorenzo Paulatto]

Again, to be checked, but I believe that just chaning Zval you can also use it 
as a Cooulomb pseudo for heavier atoms, e.g. the second row from Li onwards, 
that can be useful to do all-electron tests with QE (mind you, for second row 
you easily need 1000 Ry of ecutrho).

Any comments on this actually much appreciated,


Already for H you need several hundred Ry for a converged calculation 
(around 400-600 if I remember correctly), the reason is the divergence 
of 1/r which is an absolute pain to reproduce in plane waves.






nicola


On 08/03/2023 09:13, Paolo Giannozzi wrote:

 Forwarded Message 
Subject: Hydrogen atom pseudopotential files with q=1.5e and q=0.75e (PBE, 
USPP)
Date: Tue, 7 Mar 2023 19:58:51 +0300
From: gökhan haseki 
To: users-ow...@lists.quantum-espresso.org


Dear Quantum Espresso users, I would like to passivate the surface of a III-V 
nanowire with pseudo-Hydrogen atoms. So I need Hydrogen atom pseudopotential 
files with q=1.5e and q=0.75e (PBE, USPP). I've searched many pessupotential 
libraries but haven't been able to find it. your help and suggestions will 
guide me in this regard. Kind regards..
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Re: [QE-users] [SPAM] To calculate dielectric constant

[Lorenzo Paulatto]

On 04/03/2023 04:04, paul via users wrote:


Hi,

To calculate dielectric constant, do we have to terminate 
dangling-bond (if it exits) with H?


Best regards,

Not necessarily, but if you want the static dielectric tensor (from 
linear response in the phonon code) you absolutely need an insulator. If 
your system s metallic, you can still compute the complex dielectric 
tensor with the epsilon.x code. I don't know if what you compute would 
make sense physically, it depends on the details.


hth





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--
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IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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Re: [QE-users] I'm confused about how to use PBE0

[Lorenzo Paulatto]

Dear Malika,

the Fock exchange (also known as exact exchange) included in PBE0 is 
very computationally intensive, it is unlikely that you'll be able to 
run it on a laptop.


kind regards


On 01/03/2023 22:30, Battal Malika wrote:

Hello,
I noticed that bandgap of ZnO is underestimated when using GGA. It 
seems like PBE0 is the most accurate methode in my case to find a 
value close to the experimental one. Neverthless I don't know how to 
use it and how much time i'll need to run it in a laptop with 8 
processors.

Can you please clarify my doubts?






Malika battal
student - Qatar University

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phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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Re: [QE-users] Why my Hubbard parameter is so much bigger than what I find in the litterature?

[Lorenzo Paulatto]

se theory) because 
the 3d shell is full and in this case the approach is not suitable. 
For more details see J. Chem. Phys. 140, 121105 (2014).



HTH


Iurii


--
Dr. Iurii TIMROV
Senior Research Scientist
Theory and Simulation of Materials (THEOS)
Swiss Federal Institute of Technology Lausanne (EPFL)
CH-1015 Lausanne, Switzerland
+41 21 69 34 881
http://people.epfl.ch/265334 <http://people.epfl.ch/265334>

*From:* users  on behalf of 
NAIMI SALMA 

*Sent:* Tuesday, February 28, 2023 12:29:27 PM
*To:* Quantum ESPRESSO users Forum
*Subject:* Re: [QE-users] Why my Hubbard parameter is so much bigger 
than what I find in the litterature?

Dear Giovanni,

You`ll find attached the input files of scf1, scf2 and hp that I used 
to compute the hubbard parameter.


Can you help me to know the exact error please!




---
Salma NAIMI
PhD student - Mohamed 5 University-Rabat


*From:* users  on behalf of 
Giovanni Cantele 

*Sent:* Tuesday, February 28, 2023 12:18 PM
*To:* Quantum ESPRESSO users Forum 
*Subject:* Re: [QE-users] Why my Hubbard parameter is so much bigger 
than what I find in the litterature?

Dear Salma,

hard to say without knowing which material and atomic species you're 
dealing with. Generally speaking, if people expect a 5-6 eV U and you 
find more than 3 times more, I would suspect that an error is somwhere 
in the simulations.
You should certainly check whether you used appropriate calculation 
parameters, e.g. BZ sampling, cutoff(s), and so on.


Giovanni
--

Giovanni Cantele, PhD
CNR-SPIN
c/o Dipartimento di Fisica
Universita' di Napoli "Federico II"
Complesso Universitario M. S. Angelo - Ed. 6
Via Cintia, I-80126, Napoli, Italy
e-mail: giovanni.cant...@spin.cnr.it <mailto:giovanni.cant...@spin.cnr.it>
Phone: +39 081 676910
Skype contact: giocan74

ResearcherID: http://www.researcherid.com/rid/A-1951-2009
Web page: https://sites.google.com/view/giovanni-cantele/home


Il giorno mar 28 feb 2023 alle ore 12:04 NAIMI SALMA 
 ha scritto:


Dear experts,
I'm working on inorganic p-type semiconductor using qe-7.0 . I
want to use GGA+U, so I computed the U value by following the
steps from the HP directory/example 02 for NiO (scf1 then scf2
then then hp) without including the magnetization because my
material is not magnetic. My hubbard parameter was around 20 eV.
While the used parameter for the same material in previous papers
is around 5-6 eV ( Knowing that in previous papers they were
extracting the U parameter from the litterature). The difference
is big between their hubbard parameter and mine is that normal or
did I do something wrong?





---
Salma NAIMI
PhD student - Mohamed 5 University-Rabat

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http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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Re: [QE-users] Electronic band structure calculation for each q in ph.x

[Lorenzo Paulatto]

The phonon code needs the wave functions at each k+q point. Kind regards 

On February 27, 2023 7:45:25 a.m. GMT+01:00, KRISHNENDU MUKHERJEE 
 wrote:
>
>
>
>
>Dear pw-user, 
>
>
>
>
>I note that during ph.x calculation, electronic band structure is calculated 
>for each q. Can you please let me know why? I guess the probable reason could 
>be that, it is important to know the Fermi energy surface to calculate the 
>phonon dispersion. 
>
>
>
>
>Thank you, 
>
>Regards, 
>
>Krishnendu Mukherjee, Ph.D., 
>
>Principal Scientist, 
>
>CSIR-NML, 
>
>India. 
>
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Re: [QE-users] cell_dofree

[Lorenzo Paulatto]

"volume"
It's written quite explicitly in input_pw.txt

On February 16, 2023 7:48:54 a.m. GMT+01:00, Mpayami via users 
 wrote:
>In other words, I would like to do a general (not cubic ibrav=1) vc-relax, 
>with the constraint of keeping the space group. Just scale the axes uniformly.
>
>Mahmoud
>
>
>
>
>- Original Message -
>From: Mpayami via users (users@lists.quantum-espresso.org)
>Date: 27/11/1401 08:18
>To: Quantum ESPRESSO users Forum (users@lists.quantum-espresso.org)
>Subject: [QE-users] cell_dofree
>
>
>Dear QE Users and Developers
>
>Hi.
>I would like to do a constrained vc-relax such that only celldm(1) moves but 
>all other celldm(2), ..., celldm(6) keep fixed.
>I did not find the case in "cell_dofree" or maybe I am confused with the 
>explanations in DOC. Also I looked at init_dofree in Modules/cell_base.f90
>and still confused.
>Could anybody please help to identify the proper option?
>Thanks in advance.
>
>Best regards,
>
>
>Mahmoud Payami
>NSTRI, AEOI
>Tehran, Iran
>Email: mpay...@aeoi.org.ir
>Phone: +98(0)2182066504
>
>
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>people and expresses its concerns about the devastating
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>___
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Re: [QE-users] invalid lattice parameters error

[Lorenzo Paulatto]

Hello,

you can either use celldm — and in this case, do not forget to specify 
celldm(1) — or you can use


   CELL_PARAMETERS angstrom

but not both.


hth


On 2/15/23 15:23, Mr. Sheharyar Pervez RA FES wrote:

I am trying to do a vc-relax calculation but I keep getting the error:

     Error in routine  iosys (1):
      invalid lattice parameters ( celldm or a )


The complete input file is attached but the celldm portion of my file 
is as follows:


ibrav=12,
celldm(2)=1.150954372306601,
celldm(3)=1.7205901956662084,
celldm(4)=-2.165080936914835e-06,

I computed these values using the description in pw.x where for ibrav = 12
  12          Monoclinic P, unique axis c     celldm(2)=b/a
                                              celldm(3)=c/a,
                                              celldm(4)=cos(ab)


The values for a, b, and gamma are in the cif file:


_cell_length_a   6.62096695
_cell_length_b   7.62043086
_cell_length_c   11.39197082
_cell_angle_alpha   89.99974724
_cell_angle_beta   97.26688153
_cell_angle_gamma   90.00012405


Was there anything else I was supposed to do?



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phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
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Re: [QE-users] bad line in namelist & control: "/"

[Lorenzo Paulatto]

It is impossible to tell, as you do not provide your input.

kind regards

On 2/6/23 10:26, AISWARYA CHANDRAN wrote:
I am calculating the band structure of a compound using quantum 
espresso in a user account of a cluster. I have submitted pw_bands.in 
<http://pw_bands.in> file , scf.in <http://scf.in> file and bands.in 
<http://bands.in> file.

The output shows the error
bad line in namelist & control: "/"
The same job i submitted in my local machine using the command option 
pw.x for pw_bands.in <http://pw_bands.in> file and scf.in 
<http://scf.in> file. bands.x command for bands.in <http://bands.in> 
file and it gives output without any error.

Could you please help me to solve this problem?

Thank you

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IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
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Re: [QE-users] How to determine the ei(i) and x0(i)

[Lorenzo Paulatto]

I already based with PP/examples/ but I didn't understand how they set
ei(i) and x0(I) and nx and nx parameter on example01 and example03.



Dear Imane, these option allow you to do a plot in the plane (aka 
rectangle) that has as four vertices


x0

x0+e1

x0+e2

x0+e1+e2

You have to choose it to be parallel to the surface and at a certain 
distance from it, depending on the STM characteristics. I guess there 
could be more information on how to choose this distance in the paper.


regards






Best regards.
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phone: +33 (0)1 442 79822 / skype: paulatz
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Re: [QE-users] users Digest, Vol 186, Issue 28

[Lorenzo Paulatto]

On 31/01/2023 13:49, SPPU/05097P/2021 OYOMO BILL C wrote:
In my case the ph.x executable only produces 4 dynamical matrix files 
instead of 8 dynamical matrix files as expected since I am using 2x2x2 
qpoints.



That is true. 4 files contain 8 q-point

kind regards

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Re: [QE-users] How to grnrrate complete q-points from the reduced number of q-points by ph.x executable

[Lorenzo Paulatto]

On 1/30/23 05:46, SPPU/05097P/2021 OYOMO BILL C wrote:


Hello ,

When I run ph. x, it generates 4 q-points, and in the output, I have 
only dyn0, dyn1, dyn3 and dyn4. My request is to suggest a way to go 
out of this problem so that I can obtain all complete 8 q-points from 
the reduced number of q-points. How do I use the  q2qstqr.x executable 
to do this?




In a normal phonon calculation, all the points are generated. Each 
dynamical matrix file contains all the q-point that form a star (i.e. 
more than one, just scroll down). Using q2qstar is only necessary if for 
some reason you only have one q-point, in this case the syntax is


q2qstar.x dynfile

hth




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Re: [QE-users] "d3q" with QE7.1__d3_qq2rr.x error

[Lorenzo Paulatto]

Thank you for reporting Xin Jin,

I mistakenly forgot to put a default value for this parameter, you can 
set "-c 1" or "-c 2", it won't make any difference (I could not find any 
case where it makes a difference). Anyway, the bug is fixed already in 
development version.


Thank you for reporting.

LP

On 1/26/23 22:09, xin@mail.com wrote:


Dear QE community,

This post concerns the "d3q" and "thermal2" software working with QE.

I have installed "d3q" on both my computer and an HPC cluster, along 
with QE7.1. Although it's compiled successfully, when I run tests in 
the "examples" folder, I always get stuck at the d3_qq2rr.x calculation.


From the command line, I receive this error message:

#

Starting run at: Thu Jan 26 13:10:22 EST 2023

computing 3-body force constants

*** The MPI_Comm_f2c() function was called before MPI_INIT was invoked.

*** This is disallowed by the MPI standard.

*** Your MPI job will now abort.

[bc12109.int.ets1.calculquebec.ca:240309] Local abort before MPI_INIT 
completed completed successfully, but am not able to aggregate error 
messages, and not able to guarantee that all other processes were killed!


#

In the d3_qq2rr.out file, it shows error:

%

 Error in routine cmdline_param (1):

 required parameter not found '-c'

%

My environment is simply openmpi 4.1.2, gcc 9.5.0 (on HPC: openmpi 
4.0.3, gcc 9.3.0).


I would greatly appreciate that if someone could offer me a solution.

Best regards,

Xin Jin

Ph.D. in Energy Science and Materials

Postdoctoral Researcher

Institution: Institut National de la Recherche Scientifique

- Énergie, Matériaux et Télécommunications (INRS-EMT)


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Re: [QE-users] 回复： error in raman spectrum calculation with SOC

[Lorenzo Paulatto]

yes, at the end of the calculation you have something like:

    freq (  1 -  2) = 15.1  [cm-1]   --> E_u  L_3'   I
freq (  3 -  3) = 17.4  [cm-1]   --> A_2u L_2'   I
freq (  4 -  5) = 43.6  [cm-1]   --> E_g  L_3    R
freq (  6 -  6) = 76.0  [cm-1]   --> A_1g L_1    R
freq (  7 -  8) = 88.0  [cm-1]   --> E_u  L_3'   I
freq (  9 - 10) =    133.7  [cm-1]   --> E_u  L_3'   I
freq ( 11 - 12) =    140.9  [cm-1]   --> E_g  L_3    R
freq ( 13 - 13) =    145.3  [cm-1]   --> A_2u L_2'   I
freq ( 14 - 14) =    166.4  [cm-1]   --> A_2u L_2'   I
freq ( 15 - 15) =    179.9  [cm-1]   --> A_1g L_1    R

Where the letter I or R indicate Infrared or Raman active (you can also 
have I+R)



On 12/8/22 13:20, V Sanger via users wrote:
so I should just turn off the lraman option in ph.in and get the 
vibration modes at gamma point, and the ph.out would tell me if they 
are Raman active, right?



-- 原始邮件 --
*发件人:* "Quantum ESPRESSO users Forum" ;
*发送时间:* 2022年12月8日(星期四) 晚上8:13
*收件人:* "users";
*主题:* Re: [QE-users] error in raman spectrum calculation with SOC

Dear V(?),

you can compute vibrational frequency, ad ph.x will also determine if 
they are Raman active by symmetry. But you cannot compute the 
effective Raman cross-section. Or the anharmonic Raman spectra weight, 
but that's anotehr story.



hth


On 12/8/22 12:21, V Sanger via users wrote:
I'm trying to calculate raman spectrum with SOC. I used a 
norm-conserving fully relativistic psedopotential then the ph.out 
reported error. Does it mean that qe does not support raman 
calculation with SOC? If so, is there any other way to calculate it?


 %%
     Error in routine phq_readin (1):
     lraman, elop, and noncolin not programmed
 %%

     stopping ...

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Re: [QE-users] error in raman spectrum calculation with SOC

[Lorenzo Paulatto]

Dear V(?),

you can compute vibrational frequency, ad ph.x will also determine if 
they are Raman active by symmetry. But you cannot compute the effective 
Raman cross-section. Or the anharmonic Raman spectra weight, but that's 
anotehr story.



hth


On 12/8/22 12:21, V Sanger via users wrote:
I'm trying to calculate raman spectrum with SOC. I used a 
norm-conserving fully relativistic psedopotential then the ph.out 
reported error. Does it mean that qe does not support raman 
calculation with SOC? If so, is there any other way to calculate it?


 %%
     Error in routine phq_readin (1):
     lraman, elop, and noncolin not programmed
 %%

     stopping ...

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Re: [QE-users] No IR vibrational peak

[Lorenzo Paulatto]

Dear Janglight,

where did you expect the peak to appear exactly ?  The classification of 
peaks as IR or Raman active is in the output of phonon, which you did 
not post. The program dynmat can also give the cross-section, but you 
need to enable the calculation of dielectric constant and effective charges.


Kind regards

p.s. The square threshold of 1.d-14 is probably not tight enough.

On 28/11/2022 03:37, 홍장희 wrote:


Hi,


I was calculated ice cluster's vibration using ph.x.


but no IR peaks appeared.


I don't know the reason.


here my input & output


Normal modes for Wurtzite



tr2_ph=1.0d-14,

prefix='ice_scf',

outdir='./out/'

epsil=.false.,

trans=.true.,

asr=.true.

fildyn='dmat.ice'

/

0.0 0.0 0.0



Thanks


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Re: [QE-users] Is it possible to use different input_dft for different types of atoms

[Lorenzo Paulatto]

You can, by setting input_dft, but it is not necessarily a good idea. 
You introduce an inconsistency for no specific gain. It is however done 
routinely, e.g. for hybrid functional or semi-local VdW corrections when 
pseudopotential with the corresponding functional are not available.


cheers

On 17/11/2022 14:52, Abdeslam Houari via users wrote:
I agree, the charge density is the one of the total system, so that 
from "input_dft" it is not possible.
However, I don't know if it's possible to use different PPs for 
different atoms.  a PBE(GGA) Pseudo for atom 1 and PZ(LDA) one for 
atom 2? I did test this before !


Abdesalem Houari




On Thursday, 17 November 2022 at 02:08:17 pm GMT+1, Lorenzo Paulatto 
 wrote:



No, this would make no sense. The density functional is applied to the 
total charge density, no to the atoms.


regards


On 17/11/2022 13:56, Jibiao Li wrote:
Dear all,

I have a simple question about using "input_dft". Is it possible to 
use different input_dft for different types of atoms in a system? In 
this way, the system can be accurately described for some reasons.


Regards


Jibiao Li

Department of Materials Science and Engineering

Yangtze Normal University

Juxian Avenue 16, Fuling, Chongqing, China 408100

Scopus Research ID: 54944118000 
<https://www.scopus.com/authid/detail.uri?authorId=54944118000>


Web of Science Research ID: F-1905-2016 
<https://publons.com/researcher/2283103/jibiao-li/>




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<https://anharmonic.github.io/>

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Re: [QE-users] Is it possible to use different input_dft for different types of atoms

[Lorenzo Paulatto]

No, this would make no sense. The density functional is applied to the 
total charge density, no to the atoms.


regards


On 17/11/2022 13:56, Jibiao Li wrote:

Dear all,

I have a simple question about using "input_dft". Is it possible to 
use different input_dft for different types of atoms in a system? In 
this way, the system can be accurately described for some reasons.


Regards


Jibiao Li

Department of Materials Science and Engineering

Yangtze Normal University

Juxian Avenue 16, Fuling, Chongqing, China 408100

Scopus Research ID: 54944118000 
<https://www.scopus.com/authid/detail.uri?authorId=54944118000>


Web of Science Research ID: F-1905-2016 
<https://publons.com/researcher/2283103/jibiao-li/>




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http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
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Re: [QE-users] Compile QE 6.8

[Lorenzo Paulatto]

I would guess that your ifort installation is not configured correctly. 
Tipcally as part of the ifort installation you get a script called 
setvars.sh or someting similar, it depends on the version. Run it like


source /path/to/setvars.sh

(or variabt depending on teh version) and you should be fine.

On 16/11/2022 14:59, Riccardo Piombo uniroma1 via users wrote:


Dear comunity,

I'm trying to compile QE on ubuntu 18.04. I have followed the 
instructions written in the documentation and I have successfully 
compiled the software without any errors.


However, as soon as I try to launch any type of job the following 
error shows up:


/error while loading shared libraries: libmkl_scalapack_lp64.so: 
cannot open shared object file: No such file or directory/


It is very strange that such an error appears as ./configure did not 
report any errors.



Could someone help me out?

Thanks in advance for your help.


Riccardo Piombo

Post doc researcher in Condensed Matter Physics at Sapienza University 
of Rome



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Re: [QE-users] energy increase in nvt aimd simulation

[Lorenzo Paulatto]

nope.

we need more details


On 08/11/2022 22:59, naval singh via users wrote:

sdear all,
i am performing md simulation on 2d sytem the temperturtre fluctuation 
is coming fine but the e total with time is increasing ,

any suggestion

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Re: [QE-users] oscillations in G(V) diagram

[Lorenzo Paulatto]

Hello,

first thing, I would plot the phonon dispersion sat each volume to 
verify that they are actually nice and positive. If you have internal 
degrees of freedom, and you did not relax them, it is likely that you 
got negative phonons, which definitely breaks QHA (more or less 
catastrophically, depending on how you do it).


cheers

On 06/11/2022 16:40, Jakob Kraus wrote:

Dear QE users,


thank you very much for your comments.

To clarify: I am indeed trying to work with the QHA, and the diagrams 
with the oscillations I talked about show F(V,T) + pV as a function of 
V for a given temperature.


The system in the input files is a cubic insulator, and I calculate 
the phonon contributions in F(V,T) with the help of the phonon DOS as 
generated by successive application of


ph.x, q2r.x, and matdyn.x. The combination of total energy and 
phononic contributions is done with the help of the ASE CrystalThermo 
functionality.


The calculations for the series of volumes currently use the same 
rescaled cubic unit cell, with matching rescaled atomic positions.


I will try the cell_dofree='shape' option and keep you updated. If you 
have further suggestions, feel free to add!



Best regards,


Jakob


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Today's Topics:

    1. oscillations in G(V) diagrams (Jakob Kraus)
    2. Re: oscillations in G(V) diagrams (Lorenzo Bastonero)
    3. Re: oscillations in G(V) diagrams (Lorenzo Paulatto)


--

Message: 1
Date: Fri, 4 Nov 2022 09:20:27 +0100
From: Jakob Kraus 
To: users@lists.quantum-espresso.org
Subject: [QE-users] oscillations in G(V) diagrams
Message-ID:
<68c7ecda-68e4-bf8b-68af-ea7d03063...@physik.tu-freiberg.de>
Content-Type: text/plain; charset="utf-8"; Format="flowed"

Dear QE users,


I am trying to calculate heat capacities, and to this end, I have
calculated the Gibbs energy as a function of volume

at several temperatures in a range of 0-700 K.

However, the functions that result from this do not show a single
minimum, but rather a whole lot of oscillations, which

seem to originate from the phonons, since the E(V) diagram at 0 K shows
a single minimum as expected.

I am thankful for any help you can offer with getting rid of these
oscillations.

I have attached input files and some plots to showcase the problem.


Best regards,


Jakob Kraus, TU Freiberg
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fildyn  =   'matdyn'
zasr    =   'crystal'
flfrc   =   'force.fc'
/
-- next part --

    calculation  = 'scf'
    title    = 'Zr_BH4_4_v95'
    verbosity    = 'high'
    restart_mode = 'from_scratch'
    tstress  = .true.
    tprnfor  = .true.
    outdir   = './'
    prefix   = 'espresso'
    pseudo_dir   = '/home/kraus/pslibrary_pp/PBE_PAW'
/

    ibrav    = 1
    ecutwfc  = 120
    ecutrho  = 960
    occupations  = 'fixed'
    nspin    = 1
    ntyp = 3
    nat  = 21
    celldm(1)    = 11.718963054402725
/

    electron_maxstep = 300
    conv_thr = 1e-10
    mixing_beta  = 0.7
/

ATOMIC_SPECIES
Zr 91.224 Zr.pbe-spn-kjpaw_psl.1.0.0.UPF
B 10.81 B.pbe-n-kjpaw_psl.1.0.0.UPF
H 1.008 H.pbe-kjpaw_psl.1.0.0.UPF

K_POINTS automatic
2 2 2  0 0 0

ATOMIC_POSITIONS angstrom
Zr 3.1007040770 3.1007040770 3.1007040770
B 4.4131080846 1.7883000693 1.7883000693
B 1.7883000693 4.4131080846 1.7883000693
B 1.7883000693 1.7883000693 4.4131080846
B 4.4131080846 4.4131080846 4.4131080846
H 3.2091046915 1.6105056976 1.6105056976
H 2.9923034624 4.5909024564 1.6105056976
H 2.9923034624 1.6105056976 4.5909024564
H 3.2091046915 4.5909024564 4.5909024564
H 1.6105056976 3.2091046915 1.6105056976
H 1.6105056976 2.9923034624 4.5909024564
H 4.5909024564 2.9923034624 1.6105056976
H 4.5909024564 3.209

Re: [QE-users] oscillations in G(V) diagrams

[Lorenzo Paulatto]

Hello Jakob,

you do not give much detail about what you are doing. As said, QHA is 
effective when dealing with one degree of freedom (i.e. cubic 
semiconductor) but harder to use in any other case. Are you doing a 
constant-volume variable-cell relax (aka cell_dofree='shape') for a 
series of volumes? And then computing for each volume the Helmholtz free 
energy (from the phonons directly or from the dos)? Are you doing this 
your self by hand or using one of the available QHA software packages?


The oscillations could be an honest bug, or a difficult integration of 
the DOS.


cheers


On 04/11/2022 09:20, Jakob Kraus wrote:

Dear QE users,


I am trying to calculate heat capacities, and to this end, I have 
calculated the Gibbs energy as a function of volume


at several temperatures in a range of 0-700 K.

However, the functions that result from this do not show a single 
minimum, but rather a whole lot of oscillations, which


seem to originate from the phonons, since the E(V) diagram at 0 K 
shows a single minimum as expected.


I am thankful for any help you can offer with getting rid of these 
oscillations.


I have attached input files and some plots to showcase the problem.


Best regards,


Jakob Kraus, TU Freiberg

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Re: [QE-users] error with virtual_v2.x

[Lorenzo Paulatto]

Hello Lucian,

it is not a bug, but an error message. it is telling you that the two 
pseudopotentials need to be generated with very similar parameters (same 
r_inner) in order for the virtual_v2 code to be able to mash them 
together. At the beginning of each UPF file there should be a copy of 
the input file used to generate them, have a look if you can make sense 
of it, and tweak them to be compatible. How to do it, depends on the 
specific pseudopotentials and the code used to generate them, which you 
do not specify.


cheers

On 28/10/2022 09:13, Lucian D. Filip wrote:


Hello all,


I have encountered a weird error with virtual_v2.x in QE v7.1

I get the following when I try to mix any two US pseuso potentials:

 %%
 Error in routine Virtual (1):
 different rinner are not implemented (yet)
 %%

 stopping ...
*** The MPI_Comm_f2c() function was called before MPI_INIT was invoked.
*** This is disallowed by the MPI standard.
*** Your MPI job will now abort.
[hidra:77620] Local abort before MPI_INIT completed completed 
successfully, but am not able to aggregate error messages, and not 
able to guarantee that all other processes were killed!


On this particular machine I have installed QE 7.1 a few minutes ago 
with the linux gfortran distribution. On my cluster I have QE v7.0 
with interl fortran and I get the same thing.


I am trying to mix Ba and Sr but I get the same error for Ti and Zr. 
The last two used to work in previous versions.


Anyone know what is going on?

Cheers

--
*Dr. Lucian Dragos Filip*
National Institute of Materials Physics
Atomistilor str. 405A, PO Box MG. 7
Magurele, 077125
Bucharest, Romania
E-mail: lucian.fi...@infim.ro
Website: https://lucianfilip.wordpress.com/

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Re: [QE-users] open_grid for epsilon.x

[Lorenzo Paulatto]

Hello Aleksandra,

if you do NOT use k-points parallelization (i.e. -k 1) simulating with 
more k-points for a standard local functional will take longer, but 
won't require more resources.


Furthermore, open_grid.x is really only convenient on top of a hybrid 
functional calculation (pbe0, hse) calculation, which are much more 
expensive and where the cost of adding more k-points increases 
quadratically.


Finally, I think epsilon.x is in general a bit more expensive than pw.x, 
and less well parallelized. If you cannot run the latter with the full 
k-points grid, you probably won't be able to run the former either.


hth


On 29/10/2022 09:33, Aleksandra Oranskaia wrote:

Dear users and developers,

Did anybody succeed with the oped_grid.x code for LDA/GGA/vdw functionals?

I want to use epsilon.x for a big system (for which I do not have 
enough computational resources to switch-off the symmetry for k-grid 
in scf calculation), I am trying open_grid.x and the code does not 
seem to work.


Thank you.
--
Best wishes,
Al., phd candidate in chemical sciences
'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman)
https://cpms.kaust.edu.sa/


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Re: [QE-users] K-points, smearing and hybrid functionals in metals.

[Lorenzo Paulatto]

It could be just one case of Hartree Fock giving bad results for 
metallic systems, i.e. Phys. Rev. B 20, 1504 (1979), in particular the 
steep bands imply a vanishing DOS at the Fermi energy. But I'm not at 
all an expert of this kind of applications...


cheers

On 21/09/2022 16:54, Lorenzo Sponza wrote:


Hello everybody.

I'm having some troubles in calculating the band structure of bulk 
Iridium with HSE06. In order to do that, I'm using the 'fake k-points' 
method, so I extract the band structure from a SCF calculation using 
an home-made post-processing code which is attached to this email. I 
run each simulation in a different folder to be sure not to overwrite 
important files. I'm using the marzari-vanderbilt smearing method with 
degauss values ranging from 0.011 to 1.0 and regular k-point grids 
ranging from 2x2x2 to 12x12x12 while the fake k-points list counts 26 
k-points in all cases. You can find an example of input file attached 
to the email. In parallel I have done also some PBE calculations with 
the standard procedure SCF+BANDS.


In the case of the PBE calculation, I don't observe differences in the 
band dispersion depending on the degauss value, but the Fermi level 
moves up for higher values of degauss and the k-point convergence is 
faster.


What I observe in the case of HSE06 is that the dispersion itself does 
change depending on the degauss value. Please see the attached graphs. 
In particular, for quite "standard" values of the degauss (0.02), the 
band structure presents weird jumps crossing the Fermi level, whereas 
for high values ( degauss = 0.8 ) the dispersion is smoother across 
Fermi, converges very quickly with the regular k-point grid and looks 
somewhat similar to the PBE one. I understand it as a consequence of 
the fact that hybrids have a certain amount of EXX which act only on 
occupied states. Since the occupation is not abrupt in metals and is 
modified by the smearing, then the potential changes in a continuous 
way as a function of degauss.



Hence my questions:

- In PBE calculations, how can I know what is the right value of the 
degauss parameter? I saw answers in the forum as if it is a compromise 
between k-points and smearing amplitude and ideally an infinitely 
dense grid would give the exact result with no smearing. However this 
answer does not help me in understanding where is the right Fermi 
energy because a finer grid does not solve the issue.


- Are hybrid functionals a safe choice for the calculation of the 
electronic structure and band alignment in metals?


- Is there a rule (rigorous or rule of thumb) to set the degauss value 
in metals when using hybrid potentials?


- Am I completely wrong, and I'm just making some mistake at the level 
of scf or of the band extraction? (I have no experience on metals and 
little on hybrids)


Thanks a lot for your help !


--
Dr. Lorenzo Sponza
Chargé de Recherche au CNRS
Laboratoire d'étude de microstructures (LEM), CNRS-ONERA
29 Avenue de la division Leclerc, 92322 Châtillon
Tel: +33146734464

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Re: [QE-users] q2r with qplot

[Lorenzo Paulatto]

Hello,

q2r does Fourier transform of the dynamical matrices: it can only work 
with a uniform grid of q-points (ldisp=.true.)


If a subset of your q-points form a regular grid, or at least the 
irreducible wedge of one, you can extract those dynamical matrices, 
eventually generate the stars with q2qstar.x and then feed them to q2r.x


hth

On 18/09/2022 15:14, Aleksandra Oranskaia wrote:

Dear QE-community,

Can please someone suggest the input for q2r.x for the following case:

ph.x input

...
ldisp = .False., qplot = .True.
...
/
5
0.5 0.5 0.5 1 !1st
0.25 0.25 0.25 1
0.0 0.0 0.0 1 !2nd
0.25 0.25 0.0 1
0.5 0.5 0.0 1 !3rd

How to feed them q2r.x? I want to continue with the phonon bands 
exactly in between (0.5 0.5 0.5) - (0.0 0.0 0.0) - (0.5 0.5 0.0) using 
the calculation for five q-points, but am stuck with the q2r input.


I tried this (and other options) but it did not work:

...
/
1 1 1
5
file.G1
file.G2
file.G3
file.G4
file.G5


I will be very happy with the hints. Thank you!
--
Best wishes,
Al., phd candidate in chemical sciences
'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman)
https://cpms.kaust.edu.sa/


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Re: [QE-users] error of band-structure calculations with tpiba_c

[Lorenzo Paulatto]

ho = 451 ,
>>nspin = 2,
>>starting_magnetization(1) = -0.1,
>>starting_magnetization(2) = -0.1,
>>starting_magnetization(3) = 2.5,
>>input_dft = 'vdw-df' ,
>>  occupations = 'smearing' ,
>>  degauss = 0.02D0 ,
>> smearing = 'methfessel-paxton' ,
>>  /
>>  
>> electron_maxstep = 299,
>>  mixing_beta = 0.2D0 ,
>>  diagonalization = 'david' ,
>>  /
>> ATOMIC_SPECIES
>> O   15.999  O.pbe-n-kjpaw_psl.1.0.0.UPF
>> C   12.0107 C.pbe-n-kjpaw_psl.1.0.0.UPF
>>Fe   55.85  Fe.pbe-spn-kjpaw_psl.1.0.0.UPF
>> ATOMIC_POSITIONS angstrom
>> O 2.8664002.8664009.4012394775
>> C 2.8664002.8664008.2401634402
>> C 1.43176793951.43176793956.1720891643
>> C 1.43176793954.30103206056.1720891643
>> C 4.30103206051.43176793956.1720891643
>> C 4.30103206054.30103206056.1720891643
>> Fe0.000.006.0340426424
>> Fe0.002.8664006.0179725127
>> Fe2.8664000.006.0179725127
>> Fe2.8664002.8664006.4391387456
>> Fe1.45406686431.45406686434.3300831677
>> Fe1.45406686434.27873313574.3300831677
>> Fe4.27873313571.45406686434.3300831677
>> Fe4.27873313574.27873313574.3300831677
>> Fe0.000.002.866400   
 0
>> 0   0
>> Fe0.002.8664002.866400   
 0
>> 0   0
>> Fe2.8664000.002.866400   
 0
>> 0   0
>> Fe2.8664002.8664002.866400   
 0
>> 0   0
>> Fe1.4332001.4332001.433200   
 0
>> 0   0
>> Fe1.4332004.2996001.433200   
 0
>> 0   0
>> Fe4.2996001.4332001.433200   
 0
>> 0   0
>> Fe4.2996004.2996001.433200   
 0
>> 0   0
>> Fe0.000.000.00   
 0
>> 0   0
>> Fe0.002.8664000.00   
 0
>> 0   0
>> Fe2.8664000.000.00   
 0
>> 0   0
>> Fe2.8664002.8664000.00   
 0
>> 0   0
>> K_POINTS tpiba_c
>> 3
>> 0.0  0.0  0.0
>> 0.5  0.0  0.0
>> 0.0  0.5  0.0
>>


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Re: [QE-users] sternheimer_kernel: root not converged in phonon calculations

[Lorenzo Paulatto]

(   0.0   0.0   )
                     (   0.0   0.0   )
                     (  -0.57735   0.0   )
                     (   0.57735   0.0   )
                     (  -0.57735  -0.0   )

     Representation     4      2 modes -  To be done
     Irreps are as follows:

           mode #   5 mode #   6
           (   0.0   0.0   )  (   0.0   0.0   )
           (   0.0   0.0   )  (   0.0   0.0   )
           (   0.0   0.0   )  (   0.0   0.0   )
           (   0.0   0.0   )  (   0.0   0.0   )
           (   0.0   0.0   )  (   0.0   0.0   )
           (   0.0   0.0   )  (   0.0   0.0   )
           (  -0.53501   0.0   )  (  -0.61679   0.0   )
           (  -0.31285   0.53223   )  (  -0.26906  -0.46166   )
           (   0.22215   0.53223   )  (   0.34773  -0.46166   )

     Representation     5      1 modes -  To be done
     Irreps are as follows:

                     mode #   7
                     (   0.0   0.0   )
                     (   0.0   0.0   )
                     (   0.0   0.0   )
                     (  -0.57735   0.0   )
                     (   0.57735   0.0   )
                     (  -0.57735  -0.0   )
                     (   0.0   0.0   )
                     (   0.0   0.0   )
                     (   0.0   0.0   )

     Representation     6      2 modes -  To be done
     Irreps are as follows:

           mode #   8 mode #   9
           (  -0.40825   0.0   )  (  -0.70711   0.0   )
           (  -0.81648   0.00399   )  (  -0.1  -0.00230   )
           (  -0.40824   0.00399   )  (   0.70710  -0.00230   )
           (   0.0   0.0   )  (   0.0   0.0   )
           (   0.0   0.0   )  (   0.0   0.0   )
           (   0.0   0.0   )  (   0.0   0.0   )
           (   0.0   0.0   )  (   0.0   0.0   )
           (   0.0   0.0   )  (   0.0   0.0   )
           (   0.0   0.0   )  (   0.0   0.0   )


     PHONON       :      7.65s CPU     11.31s WALL



     Representation #   1 mode #   1

     Self-consistent Calculation
     kpoint   5 sternheimer_kernel: root not converged, thresh < 
 2.227E+03
     kpoint   6 sternheimer_kernel: root not converged, thresh < 
 1.393E+11
     kpoint  13 sternheimer_kernel: root not converged, thresh < 
 1.425E+04
     kpoint  14 sternheimer_kernel: root not converged, thresh < 
 1.223E+11
     kpoint  21 sternheimer_kernel: root not converged, thresh < 
 1.368E+10

…
     kpoint 198 sternheimer_kernel: root not converged, thresh < 
 2.098E+11
     kpoint 200 sternheimer_kernel: root not converged, thresh < 
 4.597E+03
     kpoint 203 sternheimer_kernel: root not converged, thresh < 
 3.231E+11


      iter #  17 total cpu time :    77.1 secs av.it <http://av.it>.: 
 35.1

      thresh= 1.000E-02 alpha_mix =  0.100 |ddv_scf|^2 =  2.286E+37
     kpoint   5 sternheimer_kernel: root not converged, thresh < 
 7.024E-01
     kpoint   6 sternheimer_kernel: root not converged, thresh < 
 5.781E+13
     kpoint   7 sternheimer_kernel: root not converged, thresh < 
 2.895E+07
     kpoint  12 sternheimer_kernel: root not converged, thresh < 
 3.097E+06

…
     iter #  18 total cpu time :   212.6 secs av.it <http://av.it>.:  83.3
      thresh= 1.000E-02 alpha_mix =  0.100 |ddv_scf|^2 =  4.537E+41
     kpoint   5 sternheimer_kernel: root not converged, thresh < 
 2.236E+14
     kpoint   6 sternheimer_kernel: root not converged, thresh < 
 3.750E+00
     kpoint   7 sternheimer_kernel: root not converged, thresh < 
 7.790E+14
     kpoint  13 sternheimer_kernel: root not converged, thresh < 
 3.059E+10
     kpoint  14 sternheimer_kernel: root not converged, thresh < 
 1.581E+18
     kpoint  21 sternheimer_kernel: root not converged, thresh < 
 3.527E+19

…
<<<<<<<<<<<

If more information is needed, please ask me.

Best,
Pascal



Le 28 août 2022 à 10:21, Lorenzo Paulatto  
a écrit :


Bonjour Pascal,

on which representation of which q-point does this happen?

The first rep of q-point 2 seems to converge perfectly fine on my PC.

I'd try to reproduce, but I would rather avoid repeating all the points.

cheers

On 27/08/2022 17:57, pboulet wrote:

Dear all,

I am encountering the problem mentioned in the subject of this post.

Do you know to solve this problem?

I am running ph.x on Mg2Si (not a big deal!) with NC 
pseudopotentials from dojo website.

I have optimized the structure, then ran a SCF with 60 k-points.

Here is the input for ph.x:
Mg2Si Phonon

  verbosity   = 'high',
  alpha_mix(1)= 0.1,
  tr2_ph      = 1.0d-12,
  diagonalization = 'cg',
  prefix      = 'Mg2Si',
  ldisp       = .true.,
  epsil       = .true.,
  lqdir       = .true.,
  search_sym  = .false.
  fildyn      = 'Mg2Si.dyn.xml',
  fildvscf    = 'd

Re: [QE-users] Can QE project selected electronic states of selected atoms into the k-space?

[Lorenzo Paulatto]

ongst peoples
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phone: +33 (0)1 442 79822 / skype: paulatz
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23-24/423 B115, 4 place Jussieu 75252 Paris CX 05

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phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05

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phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
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Re: [QE-users] Can QE project selected electronic states of selected atoms into the k-space?

[Lorenzo Paulatto]

I guess projwfc with option kresolveddos can project Bloch wavefunction 
of a selected k-point onto atomic reference (i.e. arbitrary) 
wavefunctions. I'm not sure that it is what you want.


> Clearly wave-functions are things in the real space not the momentum 
space.


Would you mind explaining? It is not clear to me that Bloch 
wavefunctions are real space objects. Wannier functions are clearly real 
space, but they are clearly not "wavefunctions" (i.e. they are not 
stationary states of the crystal Hamiltonian).


cheers

On 28/08/2022 12:43, Jibiao Li wrote:


Dear Lorenzo,

Thank you for your reply, but my question is "Can QEproject selected 
electronic states of selected atoms into the momentum space?" Clearly 
wave-functions are things in the real space not the momentum space.


Regards


Jibiao Li

Department of Materials Science and Engineering

Yangtze Normal University

Juxian Avenue 16, Fuling, Chongqing, China 408100

Scopus Research ID: 54944118000 
<https://www.scopus.com/authid/detail.uri?authorId=54944118000>


Web of Science Research ID: F-1905-2016 
<https://publons.com/researcher/2283103/jibiao-li/>





-- Original --
*From:* "Quantum ESPRESSO users Forum" ;
*Date:* Sun, Aug 28, 2022 06:24 PM
*To:* "users";
*Subject:* Re: [QE-users] Can QE project selected electronic states of 
selected atoms into the k-space?


Dear Jibiao,

I'm not sure if I understand your question. Quantum ESPRESSO can and 
does compute wavefunctions and Kohn-Sham energy bands at given 
k-points. It is actually the main thing it does.


kind regards


On 28/08/2022 12:13, Jibiao Li wrote:

Dear All,

In condensed matter physics, projecting electronic states of targeted 
atoms into the momentum space is definitely an important tool to 
study electronic structures of materials. I am writing this short 
email to get answer whether QE has the functionality to do like this.
May I  project either all or selected electronic states of selected 
atoms into the k-space in QE?


Regards

Jibiao Li

Department of Materials Science and Engineering

Yangtze Normal University

Juxian Avenue 16, Fuling, Chongqing, China 408100




Jibiao Li

Department of Materials Science and Engineering

Yangtze Normal University

Juxian Avenue 16, Fuling, Chongqing, China 408100

Scopus Research ID: 54944118000 
<https://www.scopus.com/authid/detail.uri?authorId=54944118000>


Web of Science Research ID: F-1905-2016 
<https://publons.com/researcher/2283103/jibiao-li/>




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phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05

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IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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Re: [QE-users] Can QE project selected electronic states of selected atoms into the k-space?

[Lorenzo Paulatto]

Dear Jibiao,

I'm not sure if I understand your question. Quantum ESPRESSO can and 
does compute wavefunctions and Kohn-Sham energy bands at given k-points. 
It is actually the main thing it does.


kind regards


On 28/08/2022 12:13, Jibiao Li wrote:

Dear All,

In condensed matter physics, projecting electronic states of targeted 
atoms into the momentum space is definitely an important tool to study 
electronic structures of materials. I am writing this short email to 
get answer whether QE has the functionality to do like this.
May I  project either all or selected electronic states of selected 
atoms into the k-space in QE?


Regards

Jibiao Li

Department of Materials Science and Engineering

Yangtze Normal University

Juxian Avenue 16, Fuling, Chongqing, China 408100




Jibiao Li

Department of Materials Science and Engineering

Yangtze Normal University

Juxian Avenue 16, Fuling, Chongqing, China 408100

Scopus Research ID: 54944118000 
<https://www.scopus.com/authid/detail.uri?authorId=54944118000>


Web of Science Research ID: F-1905-2016 
<https://publons.com/researcher/2283103/jibiao-li/>




___
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people and expresses its concerns about the devastating
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IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05___
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Re: [QE-users] sternheimer_kernel: root not converged in phonon calculations

[Lorenzo Paulatto]

Bonjour Pascal,

on which representation of which q-point does this happen?

The first rep of q-point 2 seems to converge perfectly fine on my PC.

I'd try to reproduce, but I would rather avoid repeating all the points.

cheers

On 27/08/2022 17:57, pboulet wrote:

Dear all,

I am encountering the problem mentioned in the subject of this post.

Do you know to solve this problem?

I am running ph.x on Mg2Si (not a big deal!) with NC pseudopotentials 
from dojo website.

I have optimized the structure, then ran a SCF with 60 k-points.

Here is the input for ph.x:
Mg2Si Phonon

  verbosity   = 'high',
  alpha_mix(1)= 0.1,
  tr2_ph      = 1.0d-12,
  diagonalization = 'cg',
  prefix      = 'Mg2Si',
  ldisp       = .true.,
  epsil       = .true.,
  lqdir       = .true.,
  search_sym  = .false.
  fildyn      = 'Mg2Si.dyn.xml',
  fildvscf    = 'dvscf'
  recover     = .true.,
  start_q = 2, last_q = 8,
  nq1=4, nq2=4, nq3=4,
/

and a sample of the output:
iter #  41 total cpu time :  5901.1 secs av.it <http://av.it>.: 210.4
      thresh= 1.000E-02 alpha_mix =  0.100 |ddv_scf|^2 =  1.350+100
     kpoint   3 sternheimer_kernel: root not converged, thresh < 
 3.699E+06
     kpoint   4 sternheimer_kernel: root not converged, thresh < 
 2.570E+03
     kpoint   5 sternheimer_kernel: root not converged, thresh < 
 1.322E+43
     kpoint   6 sternheimer_kernel: root not converged, thresh < 
 4.836E+01
     kpoint   7 sternheimer_kernel: root not converged, thresh < 
 2.110E-01
     kpoint  12 sternheimer_kernel: root not converged, thresh < 
 2.237E+25
     kpoint  13 sternheimer_kernel: root not converged, thresh < 
 1.420E+01
     kpoint  14 sternheimer_kernel: root not converged, thresh < 
 1.199E+21
     kpoint  15 sternheimer_kernel: root not converged, thresh < 
 6.741E+07
     kpoint  18 sternheimer_kernel: root not converged, thresh < 
 8.917E+00


Note that the calculation ran fine for the Gamma point, so in the 
present run I ‘recovered’ for k-points 2 to 8.


The input file for the SCF calculation is:

  title          = 'Mg2Si',
  calculation    = 'scf',
  etot_conv_thr  = 1d-9,
  tprnfor        = .true.,
  tstress        = .true.,
  restart_mode   = 'restart',
  verbosity      = 'high',
  prefix         = 'Mg2Si',
  wf_collect     = .true.,
/

  ibrav          = 2,
  celldm(1)      = 12.037d0,
  nat            = 3,
  ntyp           = 2,
  ecutwfc        = 100.d0,
  ecutrho        = 400.d0,
  occupations    = 'fixed',
  nbnd           = 20,
/

  conv_thr       = 1d-12,
  mixing_beta    = 0.2d0,
/
ATOMIC_SPECIES
Mg 24.3 Mg.upf
Si 28.1 Si.upf

ATOMIC_POSITIONS crystal
Si       0.0   0.0   0.0
Mg       0.25000   0.25000   0.25000
Mg       0.75000   0.75000   0.75000

K_POINTS automatic
8 8 8 1 1 1

Thank you for your help and time.
Best regards,
Pascal

.
Pascal Boulet
—
/Professor in computational materials chemistry - DEPARTMENT OF CHEMISTRY/
University of Aix-Marseille - Avenue Escadrille Normandie Niemen - 
F-13013 Marseille - FRANCE

Tél: +33(0)4 13 55 18 10 - Fax : +33(0)4 13 55 18 50
Email : pascal.bou...@univ-amu.fr





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Re: [QE-users] [SPAM] Sharp peaks at the band structure calculated with hybrid functional using the "fake" procedure

[Lorenzo Paulatto]

Hello,

I agree with you that the procedure sometimes works, sometimes it does 
not. I think the problem is that the wavefunctions at the points with 
zero weight have no variational constraint, and depending of the linear 
algebra used can converge to something sensible or not. One could try to 
modify additional_kpoint.f90 and set some small but non zero weight to 
the additional points (something in the 10^-6 to 10^-10 range). And then 
renormalize the sum of the weights.


Can you try (and most importantly test) this yourself? I won't be able 
to do any programming before a few weeks.


There are only a couple of line to change:

wk(nkstot_old+1:nkstot_old+nkstot_add) =0._dp

then, the other case :
wk(iq)=0.0d0


Instead of zero, you put a small constant. At the end, add something like
    aux = SUM(wk)
   CALL mp_sum(aux, intra_pool_sum)
   wk = wk/aux

hth

On 29/07/2022 21:49, Антон Андреевич Гавриков wrote:

Dear colleagues,
we have tried to perfom band structure DFT-calculation of crystall 
SrTiO3 with hybrid functionals.

When we run tests with silicon from the QE package it was OK.
But when we tried SrTiO3 following to the "fake" procedure in Si 
example, we've got sharp peaks in band structure graph.
We have used PBE0 and HSE functionals with US pseudopotentials. The 
result was the same.

Furthermore, despite we used  nqx1 = 2  nqx2 = 2  nqx3 = 2 in scf-input,
in scf-output there is the record:  EXX: q-point mesh:   1    1    1
Input-file:

  calculation = "scf"
  restart_mode='from_scratch',
  prefix = 'SrTiO3',
  nstep       = 900,
  max_seconds =  8.64000e+04
  pseudo_dir  = "/home/QuantumEspresso/pseudo",
  wf_collect = .true.
  etot_conv_thr   =  1.0d-8
  verbosity ='high'
/

    ibrav  = 1,
    a =  3.8931e+00,
    nat=5,
    ntyp=3,
    occupations='smearing',
    smearing   ='gauss',
    degauss    = 0.005,
    nspin= 1
    ecutwfc = 55.0d0
    ecutrho = 580.d0
    input_dft = 'hse',
    nqx1 = 2
    nqx2 = 2
    nqx3 = 2
/

    electron_maxstep = 800
    conv_thr         =  1.0d-8
    mixing_beta      =  0.3
/

ion_dynamics ='bfgs'
/

/
ATOMIC_SPECIES
O     15.9994  O.pbesol-n-rrkjus_psl.1.0.0.UPF
Sr    87.6200  Sr.pbesol-spn-rrkjus_psl.1.0.0.UPF
Ti    47.8670  Ti.pbesol-spn-rrkjus_psl.1.0.0.UPF
ATOMIC_POSITIONS {crystal}
   O           0.5           0.0           0.5
   O           0.5           0.5           0.0
   O           0.0           0.5           0.5
   Sr          0.0           0.0           0.0
   Ti           0.5           0.5           0.5
K_POINTS automatic
 8 8 8 0 0 0
ADDITIONAL_K_POINTS tpiba_b
 8
   0.00     0.00     0.00   20 ! GAMMA
   0.00     0.50     0.00   20 ! X
   0.50     0.50     0.00   28 ! M
   0.00     0.00     0.00   36 ! GAMMA
   0.50     0.50     0.50   28 ! R
   0.00     0.50     0.00    0 ! X
   0.50     0.50     0.00   20 ! M
   0.50     0.50     0.50    0 ! R
Would you answer my question, is there a way to get appropriate band 
structure picture with hybrid functional using the "fake" procedure?

Regards,
Gavrikov Anton,
PhD, researcher,
Saint-Petersburg State University.

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Re: [QE-users] Medium-entropy materials

[Lorenzo Paulatto]

Are you sure that the atoms positions are correct? Very close atoms can 
cause convergence problems. I would check with xcrysden, or the 
online-tool seekpath, or with dist.x



cheers


On 18/07/2022 15:45, Connor Wilson wrote:

Hi everyone,

I am trying to obtain a converged SCF calculation (using Quantum 
ESPRESSO, version 7.0) for the medium-entropy oxide (CoCuMgZn)_0.25 
 O. This material crystalizes in the rocksalt structure. I am using a 
64-atom supercell. I have attached my input file at the end of this 
message.


My problem is: after 50 iterations, my calculations show no trend 
towards convergence (ie. the 'estimated scf accuracies' in the pw.x 
output file stabilize around 0.5 Ry). I have made the following 
adjustments in an effort to achieve better convergence:


  * using degauss values of 0.001, 0.01, 0.02
  * using a 6 x 6 x 6 K-mesh
  * using mixing_beta of 0.05, 0.1, 0.2
  * using ecutwfc of 60, 70, 100 (each with 10x ecutrho)
  * using PBEsol, PBE pseudopotentials

My question is: do you think it is possible to achieve a converged SCF 
calculation using QE? If it is, what might an appropriate value of 
conv_thr be, and could you suggest other changes to my input file I 
could try?


Thank you for your time,


Connor Wilson
Brock University
Department of Mathematics and Science
1812 Sir Issac Brock Way, St. Catharines, ON, CAN, L2S 3A1






 pw.x input ###


  calculation = 'scf',
  prefix = 'MEO',
  tstress = .true.,
  tprnfor = .true.,
  restart_mode = 'from_scratch',
  outdir = '/home/cw279/projects/def-crandles/cw279/MEO/222c/alat'
  pseudo_dir = '/home/cw279/pseudo',
/


  ibrav = 1,
  celldm(1) = 15.1,
  nat = 64,
  ntyp = 5,
  ecutwfc = 100,
  ecutrho = 1000,
  occupations = 'smearing',
  smearing = 'mv',
  degauss = 0.01,
/


  electron_maxstep = 50,
  mixing_beta = 0.1,
  conv_thr  = 1.0d-6,
  mixing_mode = 'local-TF',
  mixing_ndim = 10,
/

ATOMIC_SPECIES
  Mg  24.305   Mg.pbe-spnl-kjpaw_psl.1.0.0.UPF
  O   15.9994  O.pbe-n-kjpaw_psl.1.0.0.UPF
  Zn  65.380   Zn.pbe-dnl-kjpaw_psl.1.0.0.UPF
  Ni  58.6934  Ni.pbe-spn-kjpaw_psl.1.0.0.UPF
  Co  58.9332  Co.pbe-spn-kjpaw_psl.0.3.1.UPF

K_POINTS {automatic}
  4 4 4  0 0 0

ATOMIC_POSITIONS {crystal}



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phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
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Re: [QE-users] problem of plottiing band structure based on hybrid HSE functional

[Lorenzo Paulatto]

...@lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users

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Re: [QE-users] Double x-coordinate in bands.x output

[Lorenzo Paulatto]

If two consecutive points are "very" far away, the bands (?) code 
assumes that you made a jump in the path and put them with the same path 
coordinate. How far is "very" far is defined i na funny way: if thw new 
step is twice as large as the previous one:


IF(dxmod >5*dxmod_save) THEN
!
!   A big jumpin dxmod is a sign that the point xk(:,n) and xk(:,n-1)
!   are quite distant and belong to two different lines. We put them on
!   the same point in the graph

(bands.f90 line 564)

You can tweak the code, or tweak your path.

cheers


On 12/07/2022 12:09, Carl-Friedrich Schön wrote:


Dear all,

I have calculated the band structure for Si with 8 atoms in the UC 
(conventional standard from MP) using QE6.4.


My input is:

///
// calculation = 'bands'//
// prefix='Si_mp-149_conventional_standard'//
// tstress = .true.//
// tprnfor = .true.//
// pseudo_dir='/rwthfs/rz/cluster/home/cs825852/DFT/UPF_Ressources_NSCF/NC'//
// outdir='tmp'//
// disk_io='low'//
// wf_collect=.true.//
/// //

// ibrav =0,//
// nat=8//
// ntyp=1//
// ecutwfc = 100//
// ecutrho = 400//
// occupations = 'fixed'//
// nbnd = 24//
/// //

// mixing_beta = 0.2//
// conv_thr = 1.0d-10//
/// //
//ATOMIC_SPECIES//
//Si 28.086 Si.upf//
//ATOMIC_POSITIONS {crystal}//
//Si  0.25  0.75  0.25//
//Si  -0.0  -0.0  0.5//
//Si  0.25  0.25  0.75//
//Si  -0.0  0.5  0.0//
//Si  0.75  0.75  0.75//
//Si  0.5  0.0  0.0//
//Si  0.75  0.25  0.25//
//Si  0.5  0.5  0.5//
//CELL_PARAMETERS//
//10.334398  0.0  0.0//
//0.0  10.334398  0.0//
//0.0  0.0  10.334398//
//K_POINTS {crystal_b}//
//12//
//0.0  0.0  0.0  20.0//
//0.5  0.0  0.5  20.0//
//0.5  0.25  0.75  20.0//
//0.375  0.375  0.75  20.0//
//0.0  0.0  0.0  20.0//
//0.5  0.5  0.5  20.0//
//0.625  0.25  0.625  20.0//
//0.5  0.25  0.75  20.0//
//0.5  0.5  0.5  20.0//
//0.375  0.375  0.75  20.0//
//0.625  0.25  0.625  20.0//
//0.5  0.0  0.5  20.0/

My bands.x output however states:

/high-symmetry point:  0. 0. 0.   x coordinate   0.//
// high-symmetry point:  0.5000 0. 0.5000   x coordinate   
0.7071//
// high-symmetry point:  0.5000 0.2500 0.7500   x coordinate   
1.0607//
// high-symmetry point:  0.3750 0.3750 0.7500   x coordinate   
1.2374//
// high-symmetry point:  0. 0. 0.   x coordinate   
1.2374//
// high-symmetry point:  0.5000 0.5000 0.5000   x coordinate   
2.1035//
// high-symmetry point:  0.6250 0.2500 0.6250   x coordinate   
2.4096//
// high-symmetry point:  0.5000 0.2500 0.7500   x coordinate   
2.5864//
// high-symmetry point:  0.5000 0.5000 0.5000   x coordinate   
2.9400//
// high-symmetry point:  0.3750 0.3750 0.7500   x coordinate   
3.2462//
// high-symmetry point:  0.6250 0.2500 0.6250   x coordinate   
3.5524//

// high-symmetry point:  0.5000 0. 0.5000   x coordinate   3.8585/

As you can see, the fourth and fifth KPoint have the same x 
coordinate, while they are not identical.


The .gnu output seems to state the correct energies, while the 
x-coordinate just stays identical for this range:


/    1.2198   -4.4150//
//    1.2286   -4.4160//
//    1.2374   -4.4163//
//    1.2374   -4.4466//
//    1.2374   -4.4594//
//    1.2374   -4.4544//
//    1.2374   -4.4316//
//    1.2374   -4.3909/

//

I had the same issue occur with Cu (mp-30).

While I have found some outputs with the same problem (?) online, it 
was the topic of the discussion.


Is this a bug, or am I missing/misunderstanding some intended behavior?

Thanks and best,

Carl-Friedrich Schön, PhD Student, RWTH Aachen


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Re: [QE-users] MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 103.

[Lorenzo Paulatto]

Dear Sui,

the error occurred before, one of the MPI copies of the pw.x code 
stopped, or crashed, then the MPI system reported this error. If you 
cannot find the pw.x output, have someone who is more expert with MPI 
help you.


kind regards


On 30/06/2022 21:55, sui xiong tay wrote:


Dear QE team and users,

I am using QE version 6.6.0 on a HPC with One Rome CPU @ 2.0GHz (32 
Cores per Node). I am currently looking into a structure attached in 
this email. However, there was an error when running the simulation 
shown below:


--

MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD

with errorcode 103.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.

You may or may not see output from other processes, depending on

exactly when Open MPI kills them.

--

There was no CRASH file but somehow the code did not seem to run.

Thank you for you help!

Shaun Tay.


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Re: [QE-users] Tc calculation in QE

[Lorenzo Paulatto]

Yes, of course. Do you expect a superconductor at 0°C or 0°F ?

Kind regards

On 28/06/2022 13:36, Soumendra Kumar Das via users wrote:

Dear QE users,
I got the TC value using lambda.x. but what is the unit of Tc. Is it 
in Kelvin ?


lambda        omega_log          T_c
   0.21767        97.920              0.000
   0.21537        97.060              0.000
   0.21593        96.007              0.000
   0.22377        92.970              0.001
   0.24450        89.024              0.003
   0.27490        86.061              0.016
   0.31033        84.280              0.056
   0.34993        83.131              0.148
   0.39310        82.425              0.313
   0.44033        81.918              0.570

*Thanks and Regards*
*Soumendra Kumar Das*
*Postdoc. Research Scholar*
*School of Physical Sciences*
*National Institute of Science Education and Research (NISER), 
**Bhubaneswar*

*PO- Bhimpur-Padanpur, Via- Jatni, District:- Khurda*
*PIN – 752050, Odisha, INDIA*

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Re: [QE-users] Fermi energy and position of dirac point in 2D electronic band structure

[Lorenzo Paulatto]

= 12,
   A = 12.305661, B = 12.305661, C = 20.0, cosAB = 0.5,
   nat = 32, ntyp = 3,            ! C=18, H=12, Pb=2
   ecutwfc = 60.0, ecutrho = 480.0,
   occupations = 'smearing', smearing = 'marzari-vanderbilt', degauss 
= 0.02205,

/

   electron_maxstep = 100,
   conv_thr =  1.0d-8,
   mixing_mode = 'plain',
   mixing_beta = 0.4, mixing_ndim = 8,
   diagonalization = 'david'
/

   ion_dynamics = 'bfgs'
/
ATOMIC_SPECIES
   Pb     207.2   Pb.pbe-dn-kjpaw_psl.0.2.2.UPF
   H      1.008   H.pbe-kjpaw_psl.1.0.0.UPF
   C     12.011   C.pbe-n-kjpaw_psl.1.0.0.UPF
ATOMIC_POSITIONS (angstrom)
      C      1.887951458      1.089922558  9.614560235
      C      1.897161739      2.478716980  9.795131247
      C      3.058056895      3.149174969  10.201826686
      C      3.094519107      0.403062014  9.798882538
      C      4.255445582      1.073514486  10.205501492
      C      4.264620685      2.462307471  10.386022641
      C      4.954605459      6.434598051  10.203602904
      C      4.954765288      7.775193715  9.796929960
      C      6.152653343      5.732466782  10.385695674
      C      6.152988872      8.476869452  9.614145680
      C      7.351027374      7.774685777  9.796148892
      C      7.350891338      6.434112052  10.202892391
      C      8.040607478      2.462414124  10.385502375
      C      8.049072424      1.074051311  10.201623729
      C      9.210124709      0.403787071  9.795016930
      C      9.247909382      3.148856515  10.204584582
      C      10.408959312      2.478560082  9.798036472
      C      10.417476033      1.090183030  9.614153988
      H      0.998237207      3.074868116  9.635193425
      H      2.991811789      4.226209592  10.358631992
      H      3.160769651      -0.673988810  9.642207163
      H      3.988739061      5.954004099  10.362184021
      H      3.989028106      8.256228576  9.638913669
      H      5.154406664      0.477394068  10.365382031
      H      7.149446547      0.478191613  10.358631345
      H      8.316631087      5.953081922  10.360913089
      H      8.316906000      8.255223371  9.637391566
      H      9.143302088      -0.672828642  9.635510075
      H      9.314642621      4.225484042  10.364079361
      H      11.308571967      3.074480176  9.641154739
     Pb      0.0      0.0  8.851674686
     Pb      6.152648942      3.552431083  11.147874419
K_POINTS (crystal_b)
   4
   0.0           0.0           0.0     30   ! Gamma
   0.7   0.3   0.0     30   ! K
   0.5           0.5           0.0     30   ! M
   0.0           0.0           0.0     30   ! Gamma

###

# post-processing bands.x


outdir = './'
prefix = 'SCF_triphenyl_Pb_OM_inf_2D_sheet_NONplanar_0.3eV_t304a',
filband = 
't304c_triphenyl_Pb_OM_inf_2D_sheet_NONp_0.3eV_kpath1.bands.dat',

lsym = .true.
/

###




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Re: [QE-users] lattice parameters using ev.x

[Lorenzo Paulatto]

If you specify "noncubic" on the second step you can just provide the volume.

kind regards
--
Lorenzo Paulatto - Paris
On Apr 4 2022, at 4:21 pm, Pooja Vyas  wrote:
> Dear users,
>
> As an input for ev.x, I've provided E-V data for tetragonal bct. In its 
> output I obtained the equilibrium volume. May I know how to extract lattice 
> parameters 'a' and 'c' from it?
>
> Regards.
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Re: [QE-users] How to compute spin projections?

[Lorenzo Paulatto]

I think if you do a non-collinear spin calculation, QE prints the spin around 
each atom on screen., i.e. :
==
atom number 1 relative position : 0. 0. 0.
charge : 9.813443
magnetization : -0.86 0.00 0.00
magnetization/charge: -0.09 0.00 0.00
polar coord.: r, theta, phi [deg] : 0.86 90.00 180.00

==

--
Lorenzo Paulatto - Paris
On Mar 30 2022, at 4:09 am, Luiz Gustavo Davanse da Silveira via users 
 wrote:
> Dear QE users and developers,
>
> For non-linear calculations VASP print out on the PROCAR file three
> othogonal spin projections at each k point of each band. Is there an way
> to obtain the same information from calculations done in QE?
>
> Best regards,
> Luiz G. D Silveira
> Associate Professor - UFPR - Brazil
>
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Re: [QE-users] IR calculation for oriented single crystal

[Lorenzo Paulatto]

Hello Zack,
the code that computes the IR cross sections is in subroutine RamanIR at line 
150 of file LR_Modules/dynmatsub.f90. If you ignore the Raman parts, it is 
literally 10 lines:

do nu = 1,3*nat
do ipol=1,3
polar(ipol)=0.0d0
end do
do na=1,nat
do ipol=1,3
do jpol=1,3
polar(ipol) = polar(ipol) + &
zstar(ipol,jpol,na)*z((na-1)*3+jpol,nu)
end do
end do
end do

infrared(nu) = 2.d0*(polar(1)**2+polar(2)**2+polar(3)**2)*irfac
... some raman stuff ...
endo do

It should be straightforward to adapt it to whatever you need. Keeping in mind 
that "zstar" is the effective charge matrix of atom "na" and z(3nat, 3nat) is 
the matrix of phonon polarizations.
Otherwise, you can have z printed by dynmat by setting the variable
fileig = 'file_name.txt'
and then do the calculation in some other way.

hth
Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05
On Mar 18 2022, at 6:23 am, Zack Gainsforth  wrote:
> Hi All,
>
> I have set up a calculation using pw.x -> ph.x -> dynmat.x successfully and 
> plotted myself an IR spectrum. The match to the experimental spectrum is 
> good. However, this is an IR spectrum assuming a powder where the photons are 
> exciting all the modes. I’d now like to calculate the spectrum for a single 
> crystal and specify the electric vector of the photon relative to the 
> crystal. It should preferentially excite certain modes.
> Is there a straightforward way to do this using ph.x + dynmat.x? Or perhaps a 
> way to read/print the dipole vectors for each mode so I can dot it with my 
> photon’s e-field? Or another way of thinking about this which is more 
> efficient? (Maybe I missed something in the documentation!)
> Thanks,
> Zack
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Re: [QE-users] on VCA for use in d3q calculation

[Lorenzo Paulatto]

Yes, but use your discretion and judgement in interpreting the results.

regards
--
Lorenzo Paulatto - Paris
On Mar 9 2022, at 12:15 am, kenneth senados  wrote:
> Dear Sir Lorenzo,
>
> Thank you.
>
> So basically, the correct way to tackle my problem is
>
> 1. Do VCA for example in GaAs_(0.9)Sb_(0.1).
> 2. Proceed with pw.x, ph.x and d3q x calculation
> 3. Consider mass disorder in As and Sb in input.TK by setting 
> isotopic_disorder=.true.
>
> This is now correct right?
>
> Thanks,
>
> Ken
> On Wed, Mar 9, 2022, 4:44 AM Lorenzo Paulatto  (mailto:paul...@gmail.com)> wrote:
> > Hello Kenneth,
> > a very important factor in the thermal conductivity of such a compound 
> > would be the mass disorder of the B and C phase. This effect is not 
> > included in the simple calculation that you are doing.
> > The simple possible way to tackle this problem, and one that is actually 
> > implemented in the d3q codes, is to consider B and C as if they where two 
> > different isotopes.
> >
> > In the input.TK file you set
> > isotopic_disorder = .true.
> >
> > and then after the namelist you specify the "isotopes" by hand:
> > ISOTOPES
> > A natural
> > B isotopes 2
> > mass_of_B (1-x)
> > mass_of_C x
> >
> > For example, let's say your material is GaAs_(0.9)Sb_(0.1)
> > ISOTOPES
> > Ga natural
> > As isotopes 2
> > 74.922 0.9
> > 121.76 0.1
> > Masses are in Dalton units (mass of C^12 = 12)
> >
> >
> >
> >
> > --
> > Lorenzo Paulatto - Paris
> >
> > On Mar 8 2022, at 5:49 pm, kenneth senados  > (mailto:kenneth.sena...@ustp.edu.ph)> wrote:
> > > Dear qe and d3q experts,
> > >
> > > I have a clarification with the d3q for thermal conductivity.
> > >
> > > Supposed I have a system i.e., A2B1-xCx where A,B and C are atoms of a 
> > > material and I did a VCA for this atom for x=0.2.
> > >
> > > I then do a pw.x, then a ph.x then a d3q.x calculation to get the thermal 
> > > k. Is it correct that the calculated k is for the A2B0.8C0.2?
> > >
> > > What about if I include the isotope scattering? Do I specify also below
> > >
> > > B isotopes 2
> > > Mass(B) 0.8
> > > Mass(C) 0.2
> > >
> > > or is the input above not necessary?
> > >
> > > Thanks,
> > >
> > > Ken
> > > Disclaimer:
> > > The information in this electronic message is privileged and 
> > > confidential, intended only for use of the individual or entity named as 
> > > addressee and recipient. If you are not the addressee indicated in this 
> > > message (or responsible for delivery of the message to such person), you 
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> > > should immediately delete this e-mail and notify the sender by reply 
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> > > other information expressed in this message are not given, nor endorsed 
> > > by and are not the responsibility of USTP unless otherwise indicated by 
> > > an authorized representative of USTP independent of this 
> > > message.___
> > > The Quantum ESPRESSO community stands by the Ukrainian
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Re: [QE-users] on VCA for use in d3q calculation

[Lorenzo Paulatto]

Hello Kenneth,
a very important factor in the thermal conductivity of such a compound would be 
the mass disorder of the B and C phase. This effect is not included in the 
simple calculation that you are doing.
The simple possible way to tackle this problem, and one that is actually 
implemented in the d3q codes, is to consider B and C as if they where two 
different isotopes.

In the input.TK file you set
isotopic_disorder = .true.

and then after the namelist you specify the "isotopes" by hand:
ISOTOPES
A natural
B isotopes 2
mass_of_B (1-x)
mass_of_C x

For example, let's say your material is GaAs_(0.9)Sb_(0.1)
ISOTOPES
Ga natural
As isotopes 2
74.922 0.9
121.76 0.1
Masses are in Dalton units (mass of C^12 = 12)

--
Lorenzo Paulatto - Paris
On Mar 8 2022, at 5:49 pm, kenneth senados  wrote:
> Dear qe and d3q experts,
>
> I have a clarification with the d3q for thermal conductivity.
>
> Supposed I have a system i.e., A2B1-xCx where A,B and C are atoms of a 
> material and I did a VCA for this atom for x=0.2.
>
> I then do a pw.x, then a ph.x then a d3q.x calculation to get the thermal k. 
> Is it correct that the calculated k is for the A2B0.8C0.2?
>
> What about if I include the isotope scattering? Do I specify also below
>
> B isotopes 2
> Mass(B) 0.8
> Mass(C) 0.2
>
> or is the input above not necessary?
>
> Thanks,
>
> Ken
> Disclaimer:
> The information in this electronic message is privileged and confidential, 
> intended only for use of the individual or entity named as addressee and 
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> effects that the Russian military offensive has on their
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> ___
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Re: [QE-users] banduppy for band unfolding

[Lorenzo Paulatto]

They were most likely done by hand. You can do these paths in a few minutes 
with any scripting program, I personally use gnu/octave, but anything that can 
do iteration, sum and multiplication will do, if operated with a brain, even MS 
excel.

--
Lorenzo Paulatto - Paris
On Mar 2 2022, at 6:04 pm, kenneth senados  wrote:
> Dear QE Users,
>
> I am studying the tutorial files for banduppy used for band unfolding.
>
> I would like to ask how this "K_POINTS crystal" below has been generated. I 
> tried kpoints.x but the kpoints below does not match with the output of 
> kpoints.x
>
> -
> K_POINTS crystal
> 84
> 0. 0. 0. 1
> 0. 0.03846154 0. 1
> 0. 0.07692308 0. 1
> 0. 0.11538462 0. 1
> 0. 0.15384615 0. 1
> 0. 0.19230769 0. 1
> 0. 0.23076923 0. 1
> 0. 0.26923077 0. 1
> 0. 0.30769231 0. 1
> 0. 0.34615385 0. 1
> 0. 0.38461538 0. 1
> 0. 0.42307692 0. 1
> 0. 0.46153846 0. 1
> 0. 0.5000 0. 1
> 0. 0.53846154 0. 1
> 0. 0.57692308 0. 1
> 0. 0.61538462 0. 1
> 0. 0.65384615 0. 1
> 0. 0.69230769 0. 1
> 0. 0.73076923 0. 1
> 0. 0.76923077 0. 1
> 0. 0.80769231 0. 1
> 0. 0.84615385 0. 1
> 0. 0.88461538 0. 1
> 0. 0.92307692 0. 1
> 0. 0.96153846 0. 1
> 0.02272727 0.02272727 0.02272727 1
> 0.02678571 0.02678571 0. 1
> 0.03125000 0. 0.03125000 1
> 0.04545455 0.04545455 0.04545455 1
> 0.05357143 0.05357143 0. 1
> 0.0625 0. 0.0625 1
> 0.06818182 0.06818182 0.06818182 1
> 0.08035714 0.08035714 0. 1
> 0.09090909 0.09090909 0.09090909 1
> 0.09375000 0. 0.09375000 1
> 0.10714286 0.10714286 0. 1
> 0.11363636 0.11363636 0.11363636 1
> 0.1250 0. 0.1250 1
> 0.13392857 0.13392857 0. 1
> 0.13636364 0.13636364 0.13636364 1
> 0.15625000 0. 0.15625000 1
> 0.15909091 0.15909091 0.15909091 1
> 0.16071429 0.16071429 0. 1
> 0.18181818 0.18181818 0.18181818 1
> 0.1875 0. 0.1875 1
> 0.1875 0.1875 0. 1
> 0.20454545 0.20454545 0.20454545 1
> 0.21428571 0.21428571 0. 1
> 0.21875000 0. 0.21875000 1
> 0.22727273 0.22727273 0.22727273 1
> 0.24107143 0.24107143 0. 1
> 0.2500 0. 0.2500 1
> 0.2500 0.2500 0.2500 1
> 0.26785714 0.26785714 0. 1
> 0.27272727 0.27272727 0.27272727 1
> 0.29464286 0.29464286 0. 1
> 0.29545455 0.29545455 0.29545455 1
> 0.31818182 0.31818182 0.31818182 1
> 0.32142857 0.32142857 0. 1
> 0.34090909 0.34090909 0.34090909 1
> 0.34821429 0.34821429 0. 1
> 0.36363636 0.36363636 0.36363636 1
> 0.3750 0.3750 0. 1
> 0.38636364 0.38636364 0.38636364 1
> 0.40178571 0.40178571 0. 1
> 0.40909091 0.40909091 0.40909091 1
> 0.42857143 0.42857143 0. 1
> 0.43181818 0.43181818 0.43181818 1
> 0.45454545 0.45454545 0.45454545 1
> 0.45535714 0.45535714 0. 1
> 0.47727273 0.47727273 0.47727273 1
> 0.48214286 0.48214286 0. 1
> 0.5000 0.5000 0.5000 1
> 0.50892857 0.50892857 0. 1
> 0.53571429 0.53571429 0. 1
> 0.5625 0.5625 0. 1
> 0.58928571 0.58928571 0. 1
> 0.61607143 0.61607143 0. 1
> 0.64285714 0.64285714 0. 1
> 0.66964286 0.66964286 0. 1
> 0.69642857 0.69642857 0. 1
> 0.72321429 0.72321429 0. 1
> 0.7500 0.7500 0. 1
>
> 
>
> any help is much appreciated.
>
> Thank you.
>
> Best regards,
>
> Ken
> Disclaimer:
> The information in this electronic message is privileged and confidential, 
> intended only for use of the individual or entity named as addressee and 
> recipient. If you are not the addressee indicated in this message (or 
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> for messages of this kind. Opinions, conclusions and other information 
> expressed in this message are not given, nor endor

Re: [QE-users] Fortran runtime error: Disk quota exceeded

[Lorenzo Paulatto]

Dear Tarek,
This is not a quantum espresso error.
Ask your system administrators to increase your disk quota, or if there is
a larger disk that you can use for storing temporary data.
Hth
-- 
Lorenzo Paulatto

On Sat, Feb 26, 2022, 03:21 Tarek Hammad  wrote:

> Dear QE team and users
>
> I run an THERMO_PW code to obtain the elastic constants for a complex
> system (40 atoms). After long time of running, namely, near the end of
> calculations the code was terminated and I have got this message in slurm
> file:
>
>
> --
>
> Job 163403 is running on comp087
> sh: gnuplot: command not found
> At line 186 of file io_base.f90 (unit = 4, file =
> './/g15/zn3p2.save/wfc59.dat')
> *Fortran runtime error: Disk quota exceeded*
>
> Error termination. Backtrace:
>
> Could not print backtrace: DWARF underflow in .debug_info at 866585
> #0  0x2b72596b2dba
> #1  0x2b72596b3875
> #2  0x2b72596b3ffa
> #3  0x2b72598abf67
> #4  0x2b72598ac090
> #5  0x2b72598ac9e8
> #6  0xb68498
> #7  0x966dda
> #8  0x9617c0
> #9  0x446820
> #10  0x47efba
> #11  0x416f26
> #12  0x4045ca
> #13  0x2b7259c68554
> #14  0x404619
> #15  0x
> --
> Primary job  terminated normally, but 1 process returned
> a non-zero exit code. Per user-direction, the job has been aborted.
> --
> --
> mpirun detected that one or more processes exited with non-zero status,
> thus causing
> the job to be terminated. The first process to do so was:
>
>   Process name: [[60482,1],0]
>   Exit code:2
>
>
> --
>
> Please, I would not like to restart from the beginning?
>
> I need your advise please.
>
> Thanks a lot for your help.
>
> Dr. Tarek Hammad.
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] users Digest, Vol 175, Issue 20

[Lorenzo Paulatto]

Tighter converge threshold, probably more k-points for a metal (you must
test it yourself, asking random people on the internet is not always
ideal), but more importantly, read my previous answer.

Regards

-- 
Lorenzo Paulatto

On Sun, Feb 20, 2022, 20:53 Naharin Jannath 
wrote:

> Hello Sally,
>
> Thanks. I modified the input script and the output was promising. But when
> I applied K  values 6 6 6 0 0 0. Pressure and cell parameters are again not
> converged. Is there anything I need to increase or decrease when I change K
> values?
>
> 
> calculation = 'vc-relax'
> restart_mode = 'from_scratch'
> prefix = 'Nb'
> etot_conv_thr = 1.d-4
> forc_conv_thr = 1.d-3
> pseudo_dir = '.'
> outdir = '.'
> disk_io = 'none'
> tstress = .true.
> tprnfor = .true.
> /
> 
> degauss = 0.05
> ecutrho = 360
> ecutwfc = 45
> ibrav   = 0
> nat = 1
> ntyp= 1
> occupations = "smearing"
> smearing= "gaussian"
> /
> 
> conv_thr =  1.0e-06
> electron_maxstep = 200
> mixing_mode  = 'plain'
> mixing_beta  =  0.2
> mixing_ndim  = 8
> startingpot  = "atomic"
> startingwfc  = "atomic+random"
> /
> 
> ion_dynamics = "bfgs"
> /
> 
> cell_dynamics = "bfgs"
> press_conv_thr = 0.01
> /
> ATOMIC_SPECIES
> Nb 92.90638 Nb.pbe-spn-kjpaw_psl.0.3.0.UPF
> ATOMIC_POSITIONS {crystal}
> Nb  0.00 0.00 0.00
> CELL_PARAMETERS {angstrom}
>  1.675751271  1.675751271  1.675751271
> -1.675751271  1.675751271  1.675751271
> -1.675751271 -1.675751271  1.675751271
> K_POINTS {automatic}
> 6 6 6  0 0 0
>
> -
>
> OUTPUT -
>
> pressure -
>   total   stress  (Ry/bohr**3)   (kbar) P=
>  -47.94
>   total   stress  (Ry/bohr**3)   (kbar) P=
>  -13.39
>   total   stress  (Ry/bohr**3)   (kbar) P=
>2.04
>   total   stress  (Ry/bohr**3)   (kbar) P=
>0.03
>   total   stress  (Ry/bohr**3)   (kbar) P=
>   -0.15
>   total   stress  (Ry/bohr**3)   (kbar) P=
>   -0.06
>   total   stress  (Ry/bohr**3)   (kbar) P=
>   -0.30
>
> CELL_PARAMETERS (angstrom)
>1.662099051   1.662099051   1.662099051
> --
> CELL_PARAMETERS (angstrom)
>1.656925425   1.656925425   1.656925425
> --
> CELL_PARAMETERS (angstrom)
>1.657605030   1.657605030   1.657605030
> --
> CELL_PARAMETERS (angstrom)
>1.657613778   1.657613778   1.657613778
> --
> CELL_PARAMETERS (angstrom)
>1.657613778   1.657613778   1.657613778
> --
> CELL_PARAMETERS (angstrom)
>1.657613778   1.657613778   1.657613778
>
> On Sun, 20 Feb 2022 at 03:00, 
> wrote:
>
>> Send users mailing list submissions to
>> users@lists.quantum-espresso.org
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> https://lists.quantum-espresso.org/mailman/listinfo/users
>> or, via email, send a message with subject or body 'help' to
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>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of users digest..."
>>
>>
>> Today's Topics:
>>
>>1. Why is my VC-RELAX not showing converged result? (Naharin Jannath)
>>2. Re: Why is my VC-RELAX not showing converged result? (sally issa)
>>3. Re: Why is my VC-RELAX not showing converged result?
>>   (Lorenzo Paulatto)
>>4. Nose-Hoover Chain in CPMD (ustbhh)
>>
>>
>> --
>>
>> Message: 1
>> Date: Sat, 19 Feb 2022 08:58:57 -0800
>> From: Naharin Jannath 
>> To: users@lists.quantum-espresso.org
>> Subject: [QE-users] Why is my VC-RELAX not showing converged result?
>> Message-ID:
>> > g1jl4dnehybnn7iczpoo2wevahmmrj7bpm7...@mail.gmail.com>
>> Content-Type: text/plain; charset="utf-8"
>>
>> I ran the VC-RELAX for simple niobium until I get a converged value. But
>> at
>> the bottom of the output, the cell parameter stops changing. Also, the
>> pressure is well below the "pres_conv_thr" which was set to 0.01 in the
>> input file. Can anyone tell me how to fix it? Also, my CELL_PARAMETER vs K
>>

Re: [QE-users] Why is my VC-RELAX not showing converged result?

[Lorenzo Paulatto]

hello,
vc-relax is done at constant fft grid, not constant kineti energy cutoff. At 
the end the scf is repeated with the initial cutoff, which can show some 
discrepancy if the calculation was not very converged, or if the initial volume 
was quite far from the final one. Repeat the vc-relax starting with the final 
cell and you should get a perfect result.

hth
--
Lorenzo Paulatto - Paris
On Feb 19 2022, at 5:58 pm, Naharin Jannath  
wrote:
> I ran the VC-RELAX for simple niobium until I get a converged value. But at 
> the bottom of the output, the cell parameter stops changing. Also, the 
> pressure is well below the "pres_conv_thr" which was set to 0.01 in the input 
> file. Can anyone tell me how to fix it? Also, my CELL_PARAMETER vs K curve is 
> not smooth even using large smearing.
>
> 
> calculation = 'vc-relax'
> restart_mode = 'from_scratch'
> prefix = 'Nb'
> etot_conv_thr = 0.01
> pseudo_dir = '.'
> outdir = '.'
> disk_io = 'none'
> tstress = .true.
> tprnfor = .true.
> /
> 
> degauss = 0.05
> ecutrho = 360
> ecutwfc = 45
> ibrav = 0
> nat = 1
> ntyp = 1
> occupations = "smearing"
> smearing = "gaussian"
> /
> 
> conv_thr = 1.0e-08
> electron_maxstep = 200
> mixing_mode = 'plain'
> mixing_beta = 0.5
> startingpot = "atomic"
> startingwfc = "atomic+random"
> /
> 
> ion_dynamics = "bfgs"
> /
> 
> cell_dynamics = "bfgs"
> press_conv_thr = 0.01
> /
> ATOMIC_SPECIES
> Nb 92.90638 Nb.pbe-spn-kjpaw_psl.0.3.0.UPF
> ATOMIC_POSITIONS {crystal}
> Nb 0.00 0.00 0.00
> CELL_PARAMETERS {angstrom}
> 1.675751271 1.675751271 1.675751271
> -1.675751271 1.675751271 1.675751271
> -1.675751271 -1.675751271 1.675751271
> K_POINTS {automatic}
> 10 10 10 0 0 0
>
>
> output --
> PRESSURE -
> total stress (Ry/bohr**3) (kbar) P= -47.02
> total stress (Ry/bohr**3) (kbar) P= -9.58
> total stress (Ry/bohr**3) (kbar) P= 0.65
> total stress (Ry/bohr**3) (kbar) P= 0.02
> total stress (Ry/bohr**3) (kbar) P= 0.01
> total stress (Ry/bohr**3) (kbar) P= -0.21
>
>
> CELL_PARAMETERS (angstrom)
> 1.662361144 1.662361144 1.662361144
> --
> CELL_PARAMETERS (angstrom)
> 1.659001159 1.659001159 1.659001159
> --
> CELL_PARAMETERS (angstrom)
> 1.659212618 1.659212618 1.659212618
> --
> CELL_PARAMETERS (angstrom)
> 1.659217666 1.659217666 1.659217666
> --
> CELL_PARAMETERS (angstrom)
> 1.659217666 1.659217666 1.659217666
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

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Re: [QE-users] Probable bug in additional_kpoints.f90 subroutine

[Lorenzo Paulatto]

Download these two files and replace those in QE7 and recompile:
https://gitlab.com/QEF/q-e/-/raw/develop/Modules/additional_kpoints.f90?inline=false
https://gitlab.com/QEF/q-e/-/raw/develop/PP/src/plotband.f90?inline=false

let me know if it does not compile
cheers

Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05
On Feb 16 2022, at 12:36 pm, Aleksandra Oranskaia 
 wrote:
> Thank you for the corrections!
>
> Where can I get the updated files (additional_kpoints.f90, plotband.f90, 
> ...?) ?
>
> --
> Best wishes,
> Alex (she/her/hers),
> phd candidate in chemical sciences
> 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman)
> https://cpms.kaust.edu.sa/
>
>
>
>
>
>
>
> This message and its contents, including attachments are intended solely for 
> the original recipient. If you are not the intended recipient or have 
> received this message in error, please notify me immediately and delete this 
> message from your computer system. Any unauthorized use or distribution is 
> prohibited. Please consider the environment before printing this 
> email.___
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Re: [QE-users] Probable bug in additional_kpoints.f90 subroutine

[Lorenzo Paulatto]

Thank you Prasenjit, I tested it and it seems correct. I also fixeda couple of 
bugs in plotbands.

Do you want to do a pull request yourself for the file ? (In that case I'ld ask 
you to remove the debug lines) or should I take care to do it?
thank you again
Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ - https://anharmonic.github.io/
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05
On Feb 15 2022, at 7:29 am, Prasenjit Ghosh  wrote:
> Dear Lorenzo and others,
>
> I think there is a bug in the above subroutine when either nqx1, nqx2 and 
> nqx3, or all of them are greater than 1. The example does not work with the 
> original version of the code because a lot of k-points with coordinates 
> (0,0,0 are generated as shown below:
>
> k( 1) = ( -0.250 0.250 0.250), wk = 0.500
> k( 2) = ( 0.250 -0.250 0.750), wk = 1.500
> k( 3) = ( 0.000 0.000 0.000), wk = 0.000
> k( 4) = ( 0.000 0.000 0.000), wk = 0.000
> k( 5) = ( 0.000 0.000 0.000), wk = 0.000
> k( 6) = ( 0.000 0.000 0.000), wk = 0.000
> k( 7) = ( 0.000 0.000 0.000), wk = 0.000
> k( 8) = ( 0.000 0.000 0.000), wk = 0.000
> k( 9) = ( 0.500 0.500 0.500), wk = 0.000
>
>
> In the above list, k-points #3 to #7 are all (0, 0,0). Because of this, when 
> running the bands.x code, it complains and stops.
>
> I was working with QE-6.8. The same problem I think persists also in 7.0.
>
> In line 89 of the subroutine, the value of the counter 'iq' seems to be 
> wrongly initialized. With this the array elements are wrongly assigned in 
> xk(:,ik). The correct one should be:
>
> iq=nkstot_old
>
> Further the array elements of 'wk', corresponding to the additional k-points 
> also need to be set to zero. This can be done right after line 98 by adding 
> the following line:
> wk(iq)=0.0d0
>
> The modified subroutine is attached.
>
> With regards,
> Prasenjit
>
>
>
> With regards,
> Prasenjit
> --
> PRASENJIT GHOSH,
> IISER Pune,
> Dr. Homi Bhabha Road, Pashan
> Pune, Maharashtra 411008, India
>
> Phone: +91 (20) 2590 8203
> Fax: +91 (20) 2589 9790
>
>
>
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

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Re: [QE-users] wrong total_weight error

[Lorenzo Paulatto]

Hello Mohamed,
probably some problem with atoms being close to but not exactly at high 
symmetry positions. Its hard to say anything as you do not provide any detail.

kind regards
--
Lorenzo Paulatto - Paris
On Feb 13 2022, at 10:48 am, Mohamed Ahmed Abd-Elati  wrote:
> Dear all
> I want to calculate the phonon dispersion for MoSiN structure.
> The steps scf, ph, and q2r have completed successfully.
> During matdyan step I faced the following error
> ...
> Error in routine frc_blk (1):
> wrong total_weight
>
> 
> I've included all of the inputs here. .
> Best regards
>
> Mohammed A. Abdelati
> Assistant Lecturer
>
> Laser Applications in Metrology Photochemistry and Agriculture (LAMPA) 
> Department, National Institute of Laser Enhanced Sciences (NILES), Cairo 
> University, Giza, Egypt.
> Mobile +20 1009752922
>
> Home +201152605076
>
> E-mail ma198...@yahoo.com (mailto:ma198...@yahoo.com)
>
>
>
>
>
>
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

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Re: [QE-users] Phonon SCF does not converge with semicore pseudopotentials

[Lorenzo Paulatto]

Did you check the electronic bands structure? Is it actually an insulator, as 
you are treating it?

hth
Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ 
(https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/0?redirect=http%3A%2F%2Fwww.impmc.upmc.fr%2F~paulatto%2F=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D)
 - https://anharmonic.github.io/ 
(https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/1?redirect=https%3A%2F%2Fanharmonic.github.io%2F=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D)
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05
On Feb 9 2022, at 8:50 am, Antonio Crepaldi  
wrote:
> Dear QE developers and users,
>
> I'm currently trying to compute the phonon dispersion of a MoTe2 bilayer with 
> QE 6.8. I'm using the stringent accuracy, FR pseudopotentials from 
> PseudoDojo, which contain semicore states for Te as well.
> I'm using vdW-DFT as vdw-df2-b86r.
> I've carefully optimized the cell and the atomic position, however the scf in 
> the phonon calculation does not converge. In fact, it seems to diverge 
> straight away:
>
> > Electric Fields Calculation
> > iter # 1 total cpu time : 118.9 secs av.it 
> > (https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/2?redirect=http%3A%2F%2Fav.it=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D).:
> >  10.2
> > thresh= 1.000E-02 alpha_mix = 0.400 |ddv_scf|^2 = 4.707E-01
> > iter # 2 total cpu time : 150.1 secs av.it 
> > (https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/3?redirect=http%3A%2F%2Fav.it=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D).:
> >  9.8
> > thresh= 1.000E-02 alpha_mix = 0.400 |ddv_scf|^2 = 1.742E+01
> > iter # 3 total cpu time : 170.5 secs av.it 
> > (https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/4?redirect=http%3A%2F%2Fav.it=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D).:
> >  4.8
> > thresh= 1.000E-02 alpha_mix = 0.400 |ddv_scf|^2 = 1.238E+01
> > iter # 4 total cpu time : 190.2 secs av.it 
> > (https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/5?redirect=http%3A%2F%2Fav.it=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D).:
> >  4.5
> > thresh= 1.000E-02 alpha_mix = 0.400 |ddv_scf|^2 = 1.133E+01
> > iter # 5 total cpu time : 210.5 secs av.it 
> > (https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/6?redirect=http%3A%2F%2Fav.it=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D).:
> >  4.8
> > thresh= 1.000E-02 alpha_mix = 0.400 |ddv_scf|^2 = 3.608E+00
> > iter # 6 total cpu time : 227.5 secs av.it 
> > (https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/7?redirect=http%3A%2F%2Fav.it=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D).:
> >  3.3
> > thresh= 1.000E-02 alpha_mix = 0.400 |ddv_scf|^2 = 4.009E+00
> > iter # 7 total cpu time : 256.9 secs av.it 
> > (https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/8?redirect=http%3A%2F%2Fav.it=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D).:
> >  9.3
> > thresh= 1.000E-02 alpha_mix = 0.400 |ddv_scf|^2 = 6.845E+01
> > iter # 8 total cpu time : 277.9 secs av.it 
> > (https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/9?redirect=http%3A%2F%2Fav.it=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D).:
> >  5.2
> > thresh= 1.000E-02 alpha_mix = 0.400 |ddv_scf|^2 = 4.813E+01
> > iter # 9 total cpu time : 297.8 secs av.it 
> > (https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/10?redirect=http%3A%2F%2Fav.it=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D).:
> >  4.8
> > thresh= 1.000E-02 alpha_mix = 0.400 |ddv_scf|^2 = 1.080E+02
>
>
> I've tried to reduce the alpha_nmix to 0.4 and 0.2 but it did not help.
> The same calculation, with proper parameters but with pseudopotentials 
> without semicore states does not give any problem.
> You can download the input and output file, as well as the pseudopotentials 
> at the following link
>
> https://www.dropbox.com/sh/zw2db8q8loczz02/AACmax-Dby-9JqZjnm1QW_LWa?dl=0 
> (https://link.getmailspring.com/link/0161e17e-5be4-499a-80cb-610ba9c07...@getmailspring.com/11?redirect=https%3A%2F%2Fwww.dropbox.com%2Fsh%2Fzw2db8q8loczz02%2FAACmax-Dby-9JqZjnm1QW_LWa%3Fdl%3D0=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D)
>
> Do you have any suggestions?
> Thank you very much for your kind help!
> Best,
>
> A

Re: [QE-users] Ce Pseudopotential (PAW) that contain 4f valence state

[Lorenzo Paulatto]

If I remember correctly, you can find this kind of pseudopotential in the
PAW_HIGH set of the pslibrary https://github.com/dalcorso/pslibrary

Again, if I remember correctly, it takes more that 100 Ry to converge it,
despite being PAW, but it works very well

-- 
Lorenzo Paulatto

On Sun, Feb 6, 2022, 11:08 Omer Mutasim via users <
users@lists.quantum-espresso.org> wrote:

> Dear All
> Greetings
> I want to do DFT+U calculation for CeO2 surface using the PAW (GGA-PBE)
> used in this article ( https://pubs.acs.org/doi/10.1021/acscatal.1c01604).
> But i couldn't find the PAW PP file for Ce  that considers 4f valence
> electrons.
> All the PP files in QE page doesn't contain 4f states, so where can i find
> it ?
> Can anyone please provide me with this Ce Pseudopotential file ?
> Regards
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] k point symmetry and open_grid.x error

[Lorenzo Paulatto]

In theory it should be possible to obtain what you need, but it is not
simple. The current open_grid code abuses some subroutine from the exact
exchange calculation, which apply symmetry to wave functions but do not do
any kind of k->k+G transformation to bring them inside the first unit cell.
Rewriting all the machinery (with all the special cases: spin, noncolinear,
parallelism, etc. ) would take a lot of time..

-- 
Lorenzo Paulatto

On Sat, Feb 5, 2022, 22:28 Zeeshan Ahmad  wrote:

> Hi,
>
> The open_grid.x code with automatic grid of k points in the scf input file
> produces k points between -0.5 and 0.5 (crystal coords). However, the EPW
> code requires wave functions for full set of k points from 0 to 1 in the
> first BZ and gives an error when using k points between -0.5 and 0.5:
>
> Error in routine epw_setup (1):
> coarse k-mesh needs to be strictly positive in 1st BZ
>
> Unfortunately this is a hybrid functional calculation, so I cannot perform
> nscf calculation or use all k points in scf due to high memory requirement.
>
> Therefore, I tried using the kpoints.x code in the PW/tools to generate
> IBZ k points between 0 and 1 and specified the weights in scf file. On
> running open_grid.x on this calculation, I get the error:
>
> Error in routine exx_grid_init (1):
>  wrong EXX q grid
>
> Is it not possible to use open_grid.x other than for automatically
> generated k-points (runs fine in that case)? And is there a way to generate
> the files for full set of k-points between 0 and 1 instead of -0.5 and 0.5?
>
> The files for reproducing the error are at:
> https://gitlab.com/ahzeeshan/qe-issues/-/tree/master/open_grid
>
> I used a 4 by 4 by 2 grid of k-points to generate the IBZ using kpoints.x
> code.
>
> Thanks for your help,
> Zeeshan
>
>
>
>
> --
> Zeeshan Ahmad
> Postdoctoral Scholar
> Pritzker School of Molecular Engineering
> The University of Chicago
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
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Re: [QE-users] Changing masses of a dynamical matrix

[Lorenzo Paulatto]

The coefficients in the dynamical matrix file, or in the force constant file, 
are not divided by 1/sqrt(M). You can change the masses in the file directly 
(in electron mass units) or use the amass(...) option of q2r/matdyn

hth
--
Lorenzo Paulatto - Paris
On Feb 3 2022, at 8:40 pm, Antoine Jay  wrote:
> Dear QE users,
> I would like to change the masses of an already calculated dynamical matrix 
> to evaluate the change in the frequencies induced by the isotopes (without 
> doing DFPT again).
> I see that dynmat and matdyn requier masses but I am wondering if the 
> starting coefficients that are saved in the .dyn file are already multiplied 
> by 1/sqrt(M_iM_j),
> or if only the diagonalized matrix (frequencies and eigenvectors) takes these 
> coefficients into account.
> Which procedure should I do?
>
> Regards,
> ---
> Antoine Jay LAAS-CNRS
> a...@laas.fr (https://www.laas.fr/public/fr/m3) 7, Avenue du Colonel Roche
> (+33)5 61 33 79 56 BP 54200, 31031 Toulouse cedex 4
> Equipe M^3 Modélisation Multi-niveaux des Matériaux
> --
>  ___
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> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

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Re: [QE-users] Crystal structure changes while doing vc-relax calculation.

[Lorenzo Paulatto]

Dear Vivek,
cell_dofree='ibrav' only works if you specified a value of ibrav>0 to begin 
with. If you don't know it, you can try to find it reading the description in 
INPUT_PW.html or with the scan_ibrav.x tool:

$ ~/espresso.BASE/PW/tools/scan_ibrav.x
Enter the unit of measur (angstrom, bohr) or alat in bohr units, or alat in Ang
strom units, followed by ' A'
19.820415
alat (bohr) 19.820415
Enter the cell basis vectors (one per line)
1.00 0.00 0.00
0.00 0.49 0.00
0.00 0.00 1.0845493931
Requested axes in Bohr units:
at1 19.820415 0.00 0.00
at2 0.00 9.910207 0.00
at3 0.00 0.00 21.496219

Scanning ibrav 1
The best cell with this ibrav is not good enough (chisq=0.8E+02)

Scanning ibrav 2
The best cell with this ibrav is not good enough (chisq=0.1E+04)

Scanning ibrav 3
The best cell with this ibrav is not good enough (chisq=0.1E+03)

Scanning ibrav -3
The best cell with this ibrav is not good enough (chisq=0.1E+04)

Scanning ibrav 4
The best cell with this ibrav is not good enough (chisq=0.8E+02)

Scanning ibrav 5
The best cell with this ibrav is not good enough (chisq=0.8E+02)

Scanning ibrav -5
The best cell with this ibrav is not good enough (chisq=0.1E+04)

Scanning ibrav 6
The best cell with this ibrav is not good enough (chisq=0.5E+02)

Scanning ibrav 7
The best cell with this ibrav is not good enough (chisq=0.1E+04)

Scanning ibrav 8
Minimization succeeded (chisq= 0. )
ibrav = 8
celldm( 1) = 19.820415000
celldm( 2) = 0.5
celldm( 3) = 1.084549393
at1 19.820415 0.00 0.00
at2 0.00 9.910207 0.00
at3 0.00 0.00 21.496219

...

Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Université
phone: +33 (0)1 442 79822 / skype: paulatz
http://www.impmc.upmc.fr/~paulatto/ 
(https://link.getmailspring.com/link/78f32a0f-3925-4a88-b3c2-dce9b9225...@getmailspring.com/0?redirect=http%3A%2F%2Fwww.impmc.upmc.fr%2F~paulatto%2F=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D)
 - https://anharmonic.github.io/ 
(https://link.getmailspring.com/link/78f32a0f-3925-4a88-b3c2-dce9b9225...@getmailspring.com/1?redirect=https%3A%2F%2Fanharmonic.github.io%2F=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D)
23-24/423 B115, 4 place Jussieu 75252 Paris CX 05
On Feb 1 2022, at 1:52 pm, Vivek Christhunathan  wrote:
> Hello Everyone,
>
> I'm bringing attention to a topic that has previously been discussed in this 
> forum. I too faced the same type of problem when I try to do structural 
> relaxation for CaWO4 (2x1x1 supercell), that its crystal structure changed 
> from Tetragonal to Orthorhombic. I tried all the following forum's 
> suggestions to get rid of this problem.
>
> As per their suggestion, I tried using the following tags in my input file,
>
> >ion_dynamics = 'damp'
> >and
> >cell_dynamics = "damp-pr"
> >which should respect the constraint.
>
> And also I tried using cell_dofree=‘ibrav'. but still lattice parameter 
> values a and b are not the same. Still, its structure changes from Tetragonal 
> to Orthorhombic.
> >You can open Modules/cell_base.f90 and at line 84 change
> >LOGICAL :: enforce_ibrav = .FALSE.! True if ibrav ...
> >to
> >LOGICAL :: enforce_ibrav = .TRUE.! True if ibrav ...
> >(do not forget to recompile pw.x) to use cell_dofree="ibrav" together with 
> >any >other cell_dofree
>
> Since I'm utilizing the Government's supercomputer cluster, I'm not sure how 
> I'd make these adjustments to the QE code. Can I get your suggestion 
> regarding this?
> >Should be present in the available patches for v.6.4.1: file
> backports-6.4.1.diff
> <https://github.com/QEF/q-e/releases/download/qe-6.4.1/backports-6.4.1.diff 
> (https://link.getmailspring.com/link/78f32a0f-3925-4a88-b3c2-dce9b9225...@getmailspring.com/2?redirect=https%3A%2F%2Fgithub.com%2FQEF%2Fq-e%2Freleases%2Fdownload%2Fqe-6.4.1%2Fbackports-6.4.1.diff=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D)>
> in https://github.com/QEF/q-e/releases 
> (https://link.getmailspring.com/link/78f32a0f-3925-4a88-b3c2-dce9b9225...@getmailspring.com/3?redirect=https%3A%2F%2Fgithub.com%2FQEF%2Fq-e%2Freleases=dXNlcnNAbGlzdHMucXVhbnR1bS1lc3ByZXNzby5vcmc%3D)
> Could you please advise me on how to proceed with this link?
>
> I have included calculations input and output for your perusal.
>
> If you could share your thoughts on this issue, that would be quite helpful.
>
> Input:
>
> 
> calculation = 'vc-relax'
> restart_mode = 'restart'
> prefix = 'CaWO4'
> tstress = .true.
> tprnfor = .true.
> pseudo_dir = './'
> outdir = './outCaWO4'
> wf_collect=.true.
> forc_conv_thr = 1d-4
> etot_conv_thr = 1D-4
> !disk_io = 'medium'
> max_seconds = 7200,
> /
>
> 
> ibrav = 0
> celldm(1) = 19.820415
> nat = 48
>

Re: [QE-users] Does QE contain any OpenMP optimization ?

[Lorenzo Paulatto]

Most of the computationally expensive parts of QE have been progressively 
extracted from the code in the form of "libraries", which are parallelized both 
with MPI and openmp and mostly support GPU. Please have a look at this paper: 
https://arxiv.org/abs/2104.10502
kind regards
--
Lorenzo Paulatto - Paris
On Jan 29 2022, at 10:16 pm, Husak Michal  wrote:
> Hi
>
>
> I was comparing the speed of QE build with
> --enable-openmp
> and
> --disable-openmp
> MPI was disabled ...
>
> From what I see OpenMP is activated but the speed gain is zero ...
> I was searching for OpenMP optimization flags in QE fortran code like
> !$OMP PARALLEL etc ...
> But I did not find any in important source codes ...
> Did I not catch something or is there really no OpenMP optimization in QE and 
> eventual MP speed up can be obtained only by the use of external (linear 
> algebra, fft) libraries ?
> Michal Husak UCT Prague
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> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>

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Re: [QE-users] new qe superfeatures

[Lorenzo Paulatto]

Hello, if I did not introduce any bug, it should add (20+20+1)x(2x2x2)=328 
points, they should trace 8 paths in the BZ each one shifted by one of the 
q-point w.r.t the requested one. But the way the EXX code work is a bit 
complicated, and I cannot exclude with 100% confidence that there is no bug.

hth
--
Lorenzo Paulatto - Paris
On Jan 26 2022, at 6:17 pm, Aleksandra Oranskaia 
 wrote:
> Can please somebody explain how "additional k points" work? For example, for 
> 2 2 2 in nqx, 6 6 6 in dft and additional points in crystal_b:
> 3
> 0.0 0.0 0.0 20
> 0.5 0.0 0.0 20
> 0.5 0.5 0.5 1
> How many points will be calculated and how?
>
> I would highly appreciate any comments/explanations.
>
> Thank you!
> ---
> Best wishes,
> Alex (she/her/hers),
> phd candidate in chemical sciences
> 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman)
> https://cpms.kaust.edu.sa/
>
>
>
>
>
>
>
>
>
>
> This message and its contents, including attachments are intended solely for 
> the original recipient. If you are not the intended recipient or have 
> received this message in error, please notify me immediately and delete this 
> message from your computer system. Any unauthorized use or distribution is 
> prohibited. Please consider the environment before printing this 
> email.___
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Re: [QE-users] new qe superfeatures

[Lorenzo Paulatto]

I have received it. I have the impression when pw.x add the k+q points, or when 
simmetry is applied, the order of k-points is not what the example expects, but 
the information is there. I do not have time to work on this issue before a few 
days.

htht
--
Lorenzo Paulatto - Paris
On Jan 23 2022, at 8:58 am, Aleksandra Oranskaia 
 wrote:
> Dear Prof Lorenzo (Paulatto),
>
> I summarized the messages above and sent to the email shown in your reply 
> (paulatz at googlemail), please check your spam folder if you have not 
> received it.
>
> Thank you for helping!
>
> --
> Best wishes,
> Alex (she/her/hers),
> phd candidate in chemical sciences
> 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman)
> https://cpms.kaust.edu.sa/
>
>
>
>
>
>
>
> This message and its contents, including attachments are intended solely for 
> the original recipient. If you are not the intended recipient or have 
> received this message in error, please notify me immediately and delete this 
> message from your computer system. Any unauthorized use or distribution is 
> prohibited. Please consider the environment before printing this 
> email.___
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> users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] Choice of awin for average.x calculations

[Lorenzo Paulatto]

Hello,
I do not have an answer to your question, I have never used average.x.

However, when there is a parameter I need to choose, this is my procedure:
identify a physical range of values

try a few values in between

compare to see if it makes any difference
and if necessary:

try to understand the differences, which applies to my case

hth
--
Lorenzo Paulatto - Paris
On Jan 21 2022, at 4:02 pm, Anson Thomas  wrote:
> Dear QE Users,
>
> I have a general (and maybe naive) question to ask. What value should we 
> choose for awin for average.x calculations?
> Any insights on this would be appreciated.
>
> Thank you
>
>
> --
> Anson Thomas
> M.Sc. Chemistry, IIT Roorkee
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
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Re: [QE-users] new qe superfeatures

[Lorenzo Paulatto]

Here I am, what's the problem?

-- 
Lorenzo Paulatto

On Tue, Jan 18, 2022, 19:07 Aleksandra Oranskaia <
aleksandra.oransk...@kaust.edu.sa> wrote:

> Yep it is a bug (i asked smart people to run the example).
>
> In reference folder the address for the pseudos was:
> /home/paulatto/espresso/pseudo/
> so probably 'paulatto' is the developer to contact.
> Can please somebody share his/her full name or contacts?
>
> --
> Best wishes,
> Alex (she/her/hers),
> phd candidate in chemical sciences
> 'I.. a universe of atoms, an atom in the universe' (Richard P. Feynman)
> https://cpms.kaust.edu.sa/
>
> --
> This message and its contents, including attachments are intended solely
> for the original recipient. If you are not the intended recipient or have
> received this message in error, please notify me immediately and delete
> this message from your computer system. Any unauthorized use or
> distribution is prohibited. Please consider the environment before printing
> this email.___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
___
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