date:20230608

[QE-users] error executing the d3_q2r.x

2023-06-08 Thread Elio Physics

Dear  all,

This post concerns the "d3q" and "thermal2" codes:

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 2nd 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
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[QE-users] scf convergence

2023-06-08 Thread Ramon Sampaio Ferreira

Hello everyone,

I hope everyone is doing well.

I am confused about the convergence of the system I'm testing. The problem
is the following: at the beginning of the simulation, apparently everything
was going well, but some warning messages appeared and I was a little
afraid if everything is ok with the convergence process.

The first warning message is as follows (a lot of them):

iteration #126 ecut=   100.00 Ry beta= 0.10
 Davidson diagonalization with overlap
 c_bands:  4 eigenvalues not converged
 c_bands:  1 eigenvalues not converged
 c_bands:  3 eigenvalues not converged

and the other one:

 WARNING: integrated charge=   228.3355, expected=   228.

My questions are:

->Should I just ignore these messages and continue with the convergence
process?

->What could I modify in the input file to improve the convergence process?

->I am simulating a primitive cell, if I want to simulate a supercell (say
2x2x2), doing the SCF calculation and after that the phonon calculation,
what convergence parameters should I modify in the initial input file?
Reduce ecutwfc, conv_thr, mixing_beta and k-points, for example?

I greatly appreciate any help you can provide. Thank you so much!

The input file is below:


  calculation = 'scf'
  restart_mode = 'from_scratch'
  outdir = './
  prefix = 'Ce2WO43'
  pseudo_dir = './'
 /

  degauss =   1.00d-03
  ecutwfc =   10.00d+01
  ibrav = 0
  nat = 34
  ntyp = 3
  occupations = 'smearing'
  smearing = 'methfessel-paxton'
/

   conv_thr =   1.0d-09
   electron_maxstep = 1000
   mixing_beta =   1.00d-01
/
ATOMIC_SPECIES
Ce 140.116 Ce.pz-sp-hgh.UPF
O  15.9994 O.pz-hgh.UPF
W  183.840 W.pz-hgh.UPF
ATOMIC_POSITIONS crystal
Ce   0.712100   0.042551   0.405127
Ce   0.042551   0.712100   0.094873
Ce   0.287900   0.957449   0.594873
Ce   0.957449   0.287900   0.905127
W0.865642   0.865642   0.75
W0.134358   0.134358   0.25
W0.540379   0.252745   0.046477
W0.252745   0.540379   0.453523
W0.459621   0.747255   0.953523
W0.747255   0.459621   0.546477
O0.471875   0.603629   0.570964
O0.603629   0.471875   0.929036
O0.528125   0.396371   0.429036
O0.396371   0.528125   0.070964
O0.340281   0.231175   0.940361
O0.231175   0.340281   0.559639
O0.659719   0.768825   0.059639
O0.768825   0.659719   0.440361
O0.889232   0.454564   0.695605
O0.454564   0.889232   0.804395
O0.337723   0.081921   0.390609
O0.081921   0.337723   0.109391
O0.662277   0.918079   0.609391
O0.918079   0.662277   0.890609
O0.883783   0.206903   0.281126
O0.206903   0.883783   0.218874
O0.116217   0.793097   0.718874
O0.793097   0.116217   0.781126
O0.084356   0.811465   0.460370
O0.811465   0.084356   0.039630
O0.915644   0.188535   0.539630
O0.188535   0.915644   0.960370
O0.545436   0.110768   0.195605
O0.110768   0.545436   0.304395
K_POINTS automatic
10 10 10 0 0 0
CELL_PARAMETERS angstrom
  7.1400620600   0.00   0.00
  2.6686708410   6.6225887811   0.00
 -2.2226301817   3.2919431525  11.0483089965
___
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] asr in dynmat.x

2023-06-08 Thread Juliana Maria Abreu Da Silva Morbec

Thanks, Paolo and Lorenzo, for your comments.
I will do some tests for the threshold.
But let me point out that this is bulk MoS2, not 2D.

Regards,

Juliana
-
Dr Juliana Morbec
Lecturer in Physics
Keele University, UK

From: Lorenzo Bastonero 
Sent: Thursday, June 8, 2023 10:22:39 AM
To: Quantum ESPRESSO users Forum 
Cc: Juliana Maria Abreu Da Silva Morbec 
Subject: Re: [QE-users] asr in dynmat.x

Dear Juliana,

Indeed the ASR in the old QE version did not include the correct rotational 
invariants for 2D systems, i.e. you should have 4 acoustic modes at Gamma that 
are zero.

Although, having a closer look to your inputs, I would suggest you to pay 
attention to:
1. Why have you commented out ‘assume_isolated’? That is usually important to 
get rid of the long-range planar interaction between images.
2. The threshold for phonons seem a bit too low. Did you do some tests? In my 
experience that threshold should be much lower, e.g. 1e-16/18.

HTH,
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 8 giu 2023, alle ore 11:08, Paolo Giannozzi 
mailto:paolo.gianno...@uniud.it>> ha scritto:

I have heard that in 2D systems some acoustic sum rules may yield funny results 
for acoustic modes close to q=0. The latest 7.2 version of the code should 
contain an improved ASR. See https://gitlab.com/QEF/q-e/-/merge_requests/1978

Paolo

On 6/8/23 00:12, Juliana Maria Abreu Da Silva Morbec wrote:

You don't often get email from 
j.mor...@keele.ac.uk. Learn why this is important 


Dear Lorenzo.
Thanks for your response.
I am attaching here the input files for scf and phonon calculations of bulk 
MoS2, as well as output files of dynmat.x using asr='simple' and asr='crystal'. 
I also noticed that asr='no' give similar results to asr='crystal'.
Regards,
Juliana
-
*Dr Juliana Morbec*
Lecturer in Physics
Keele University, UK

*From:* users 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Lorenzo Bastonero 
mailto:lbast...@uni-bremen.de>>
*Sent:* 06 June 2023 14:28
*To:* Quantum ESPRESSO users Forum 
mailto:users@lists.quantum-espresso.org>>
*Subject:* Re: [QE-users] asr in dynmat.x
Dear Juliana,
In principle at Gamma the acoustic sum rules should only affect the 3 acoustic 
modes, setting them to 0, and leave the other modes close to their values ( ~< 
1/0.1 cm-1).
If you are experiencing huge change in the wavenumber, it may probably be a 
sign of under converged calculations. Hard to say though w/o inputs/outputs.
HTH,
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 6 giu 2023, alle ore 15:14, Juliana Maria Abreu Da Silva Morbec 
mailto:j.mor...@keele.ac.uk> 
> ha scritto:

Hello.

I have a question regarding the 'asr' feature in dynmat.x. I am computing Raman 
spectra of MoS2 bulk and I noticed that asr='simple' and asr='crystal' give 
different frequencies but similar amplitude for Raman. And asr='crystal' seems 
to be in better agreement with experiments. How to decide which one to use?

Thank you,

Juliana Morbec
Lecturer in Physics
Keele University, UK
--
Please consider the environment before printing this email.This email and its 
contents may be legally privileged and /or confidential.If it has come to you 
in error you should not copy or show it to anyone; nor should you take any 
action based on it, other than to reply to the sender to notify them of the 
error immediately and to then delete the email from your inbox and deleted 
items. Keele University staff and students are required to abide by the 
University's IT Policies when sending and receiving email. Keele University 
email is hosted by a cloud provider and may be stored outside of the UK.
___
The Quantum ESPRESSO community stands by the Ukrainian
people and expresses its concerns about the devastating

Re: [QE-users] asr in dynmat.x

2023-06-08 Thread Lorenzo Bastonero

Dear Juliana,

Indeed the ASR in the old QE version did not include the correct rotational 
invariants for 2D systems, i.e. you should have 4 acoustic modes at Gamma that 
are zero.

Although, having a closer look to your inputs, I would suggest you to pay 
attention to:
1. Why have you commented out ‘assume_isolated’? That is usually important to 
get rid of the long-range planar interaction between images.
2. The threshold for phonons seem a bit too low. Did you do some tests? In my 
experience that threshold should be much lower, e.g. 1e-16/18.

HTH,
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 8 giu 2023, alle ore 11:08, Paolo Giannozzi 
>  ha scritto:
> 
> I have heard that in 2D systems some acoustic sum rules may yield funny 
> results for acoustic modes close to q=0. The latest 7.2 version of the code 
> should contain an improved ASR. See 
> https://gitlab.com/QEF/q-e/-/merge_requests/1978 
> 
> 
> Paolo
> 
> On 6/8/23 00:12, Juliana Maria Abreu Da Silva Morbec wrote:
>>  
>> You don't often get email from j.mor...@keele.ac.uk 
>> . Learn why this is important 
>> > >
>>  
>> Dear Lorenzo.
>> Thanks for your response.
>> I am attaching here the input files for scf and phonon calculations of bulk 
>> MoS2, as well as output files of dynmat.x using asr='simple' and 
>> asr='crystal'. I also noticed that asr='no' give similar results to 
>> asr='crystal'.
>> Regards,
>> Juliana
>> -
>> *Dr Juliana Morbec*
>> Lecturer in Physics
>> Keele University, UK
>> 
>> *From:* users  on behalf of 
>> Lorenzo Bastonero 
>> *Sent:* 06 June 2023 14:28
>> *To:* Quantum ESPRESSO users Forum 
>> *Subject:* Re: [QE-users] asr in dynmat.x
>> Dear Juliana,
>> In principle at Gamma the acoustic sum rules should only affect the 3 
>> acoustic modes, setting them to 0, and leave the other modes close to their 
>> values ( ~< 1/0.1 cm-1).
>> If you are experiencing huge change in the wavenumber, it may probably be a 
>> sign of under converged calculations. Hard to say though w/o inputs/outputs.
>> HTH,
>> 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 6 giu 2023, alle ore 15:14, Juliana Maria Abreu Da Silva Morbec 
>>> mailto:j.mor...@keele.ac.uk> 
>>> >> ha scritto:
>>> 
>>> Hello.
>>> 
>>> I have a question regarding the 'asr' feature in dynmat.x. I am computing 
>>> Raman spectra of MoS2 bulk and I noticed that asr='simple' and 
>>> asr='crystal' give different frequencies but similar amplitude for Raman. 
>>> And asr='crystal' seems to be in better agreement with experiments. How to 
>>> decide which one to use?
>>> 
>>> Thank you,
>>> 
>>> Juliana Morbec
>>> Lecturer in Physics
>>> Keele University, UK
>>> --
>>> Please consider the environment before printing this email.This email and 
>>> its contents may be legally privileged and /or confidential.If it has come 
>>> to you in error you should not copy or show it to anyone; nor should you 
>>> take any action based on it, other than to reply to the sender to notify 
>>> them of the error immediately and to then delete the email from your inbox 
>>> and deleted items. Keele University staff and students are required to 
>>> abide by the University's IT Policies when sending and receiving email. 
>>> Keele

Re: [QE-users] asr in dynmat.x

2023-06-08 Thread Paolo Giannozzi

I have heard that in 2D systems some acoustic sum rules may yield funny 
results for acoustic modes close to q=0. The latest 7.2 version of the 
code should contain an improved ASR. See 
https://gitlab.com/QEF/q-e/-/merge_requests/1978


Paolo

On 6/8/23 00:12, Juliana Maria Abreu Da Silva Morbec wrote:


You don't often get email from j.mor...@keele.ac.uk. Learn why this is 
important 



Dear Lorenzo.

Thanks for your response.
I am attaching here the input files for scf and phonon calculations of 
bulk MoS2, as well as output files of dynmat.x using asr='simple' and 
asr='crystal'. I also noticed that asr='no' give similar results to 
asr='crystal'.


Regards,

Juliana
-
*Dr Juliana Morbec*
Lecturer in Physics
Keele University, UK

*From:* users  on behalf of 
Lorenzo Bastonero 

*Sent:* 06 June 2023 14:28
*To:* Quantum ESPRESSO users Forum 
*Subject:* Re: [QE-users] asr in dynmat.x
Dear Juliana,

In principle at Gamma the acoustic sum rules should only affect the 3 
acoustic modes, setting them to 0, and leave the other modes close to 
their values ( ~< 1/0.1 cm-1).


If you are experiencing huge change in the wavenumber, it may probably 
be a sign of under converged calculations. Hard to say though w/o 
inputs/outputs.


HTH,
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 6 giu 2023, alle ore 15:14, Juliana Maria Abreu Da Silva 
Morbec mailto:j.mor...@keele.ac.uk>> ha scritto:


Hello.

I have a question regarding the 'asr' feature in dynmat.x. I am 
computing Raman spectra of MoS2 bulk and I noticed that asr='simple' 
and asr='crystal' give different frequencies but similar amplitude for 
Raman. And asr='crystal' seems to be in better agreement with 
experiments. How to decide which one to use?


Thank you,

Juliana Morbec
Lecturer in Physics
Keele University, UK
--
Please consider the environment before printing this email.This email 
and its contents may be legally privileged and /or confidential.If it 
has come to you in error you should not copy or show it to anyone; nor 
should you take any action based on it, other than to reply to the 
sender to notify them of the error immediately and to then delete the 
email from your inbox and deleted items. Keele University staff and 
students are required to abide by the University's IT Policies when 
sending and receiving email. Keele University email is hosted by a 
cloud provider and may be stored outside of the UK.

___
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
___
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 



--
Please consider the environment before printing this email.This email 
and its contents may be legally privileged and /or confidential.If it 
has come to you in error you should not copy or show it to anyone; nor 
should you take any action based on it, other than to reply to the 
sender to notify them of the error immediately and to then

[QE-users] error executing the d3_q2r.x

[QE-users] scf convergence

Re: [QE-users] asr in dynmat.x

Re: [QE-users] asr in dynmat.x

Re: [QE-users] asr in dynmat.x

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