Re: [QE-users] Band calculations for 2x2x2 supercell- stops after a while

[Paolo Giannozzi]

On Fri, Feb 4, 2022 at 8:10 AM Pietro Bonfa'  wrote:

>
> Do not use openMP, use MPI.
>

well, one may use OpenMP as well, but
- it is typically less efficient than MPI parallelization,
- 32 threads per MPI process are too many, and
- support for OpenMP in old versions (6.4.1) is not great

Paolo
-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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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] Band calculations for 2x2x2 supercell- stops after a while

[Pietro Bonfa']

Dear Srihari,

your problem is in the parallel execution:

On 2/4/22 07:57, Srihari Venugopala Rao wrote:

      Parallel version (MPI & OpenMP), running on       32 processor cores
      Number of MPI processes:                 1
      Threads/MPI process:                     32


Do not use openMP, use MPI. Your execution should look something like this

   export OMP_NUM_THREADS=1
   mpirun -np 16 /path/to/pw.x -inp input > output

The output should look something like this:

   Parallel version (MPI & OpenMP), running on   16 processor cores
   Number of MPI processes: 16
   Threads/MPI process: 1


Further optimization may be obtained with the -npool option (see user 
guide).


Best,
Pietro
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[QE-users] Band calculations for 2x2x2 supercell- stops after a while

[Srihari Venugopala Rao]

Dear all,
I have previously completed the band calculations of the BIFeO3
unit cell, and was planning to do the same for the 2x2x2 supercell. But the
band calculations stops after some time, I have left the program  run for a
week, with no use.
The system I use is AMD ryzen 16 core 3900x with 32 GB RAM with ample
storage space, with windows, I am pasting the input and the output script
for your reference.

/*Input*/
&CONTROL
calculation = "bands"
prefix='bfo'
max_seconds =  8.64000e+13
pseudo_dir  = "."
outdir='data'
verbosity = "high"
/

&SYSTEM
a =  1.140784672e+01
   cosab =  5.15505e-01
degauss   =  1.0e-02
ecutrho   =  6.50e+02
ecutwfc   =  13.0e+01
ibrav = 5
nat   = 80
nspin = 2
ntyp  = 3
occupations   = "smearing"
smearing  = "gaussian"
starting_magnetization(1) =  1.0e-01
starting_magnetization(2) =  0.0e+00
starting_magnetization(3) =  0.0e+00
/

&ELECTRONS
conv_thr =  1.0e-09
electron_maxstep = 200
mixing_beta  =  4.0e-01
startingpot  = "atomic"
startingwfc  = "atomic+random"
/


K_POINTS {tpiba_b}
13
gG 20
L  20
B1 0
B  20
Z  20
gG 20
X  0
Q  20
F  20
P1 20
Z  0
L  20
P  0

ATOMIC_SPECIES
Fe 55.84500  Fe.UPF
Bi208.98038  Bi.UPF
O  15.99940  O.UPF

ATOMIC_POSITIONS (angstrom)
Fe  -0.0  -0.0  11.045878099
Fe  -0.0  -0.0   3.998566253
Bi  -0.0  -0.0   7.059813239
Bi   0.0  -0.0   0.012497444
O1.241352350   2.023428436   7.697449126
O1.131663690  -2.086756173   7.697449126
O   -2.373016040   0.063328731   7.697449126
O1.549243260   0.412276810   5.348345854
O   -0.417579446  -1.547822381   5.348345854
O   -1.131662819   1.135545571   5.348345854
Fe  -2.790593888  -1.611150697  15.744086326
Fe  -2.790594718  -1.611150556   8.696773378
Bi  -2.790594144  -1.611150834  11.758020384
Bi  -2.790594557  -1.611149915   4.710706266
O   -1.549242716   0.412278665  12.395656350
O   -1.658930251  -3.697907125  12.395655702
O   -5.163608971  -1.547822802  12.395658709
O   -1.241350884  -1.198873760  10.046552446
O   -3.208173434  -3.158973657  10.046553141
O   -3.922257963  -0.475606384  10.046553098
Fe  -0.00430   3.222300650  15.744086326
Fe   0.00107   3.222301298   8.696773378
Bi  -0.00421   3.222300940  11.758020384
Bi   0.00581   3.222300838   4.710706266
O1.241351579   5.245728178  12.395658709
O1.131664155   1.135544173  12.395656350
O   -2.373016664   3.285629555  12.395655702
O1.549241872   3.634578316  10.046553098
O   -0.417579274   1.674478062  10.046552446
O   -1.131664197   4.357845736  10.046553141
Fe  -2.790594293   1.611149994  20.442294422
Fe  -2.790594627   1.611150727  13.394981082
Bi  -2.790594530   1.611150062  16.456227720
Bi  -2.790593949   1.611150974   9.408915551
O   -1.549243632   3.634578296  17.093866201
O   -1.658929399  -0.475606604  17.093863236
O   -5.163609573   1.674478723  17.093865610
O   -1.241352146   2.023428769  14.744760055
O   -3.208173300   0.063327162  14.744760118
O   -3.922258965   2.746694102  14.744760746
Fe   2.790594318  -1.611149953  15.744086326
Fe   2.790594611  -1.611150742   8.696773378
Bi   2.790594564  -1.611150106  11.758020384
Bi   2.790593975  -1.611150922   4.710706266
O4.031946915   0.412278564  12.395655702
O3.922258386  -3.697905377  12.395658709
O0.417577567  -1.547822838  12.395656350
O4.339837631  -1.198873073  10.046553141
O2.373016092  -3.158971932  10.046553098
O1.658930158  -0.475604302  10.046552446
Fe   0.00383  -3.222300649  20.442294422
Fe  -0.00085  -3.222301305  13.394981082
Bi   0.00441  -3.222300888  16.456227720
Bi  -0.00639  -3.222300842   9.408915551
O1.241352497  -1.198871952  17.093863236
O1.131663694  -5.309056163  17.093865610
O   -2.373015195  -3.158973446  17.093866201
O1.549244176  -2.810022870  14.744760118
O   -0.417577368  -4.770123042  14.744760746
O   -1.131664080  -2.086756164  14.744760055
Fe   2.790593912   1.611150656  20.442294422
Fe   2.790594712   1.611150579  13.394981082
Bi   2.790594090   1.611150826  16.456227720
Bi   2.790594588   1.611149868   9.408915551
O4.031945879   3.634578434  17.093865610
O3.922258827  -0.475604850  17.093866201
O0.417576901   1.674478555  17.093863236
O4.339836332   2.023428940  14.744760746
O2.373016228   0.063328388  14.744760055
O1.65

Re: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm OpenMPI).

[Husak Michal]

For sure I only edited ENVIRONMENT ...
The acces from browser was only an experiment ...
This did not make the download functional through
make run-tests
anyway
Does it work from your enviroment ?

From: users  on behalf of Ye Luo 

Sent: Friday, February 4, 2022 1:29:27 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm 
OpenMPI).

I only said edit ENVIRONMENT. The download script will add the pseudopotential 
file name to NETWORK_PSEUDO and download the file.
https://www.quantum-espresso.org/wp-content/uploads/upf_files/ is not a website.
Then `make run-tests-pw-parallel` will work.
Ye
===
Ye Luo, Ph.D.
Computational Science Division & Leadership Computing Facility
Argonne National Laboratory


On Thu, Feb 3, 2022 at 5:48 PM Husak Michal 
mailto:michal.hu...@vscht.cz>> wrote:
Hi


This does not work.

The link bellow is not accessible in any mode ...

https://www.quantum-espresso.org/wp-content/uploads/upf_files/

Forbidden

You don't have permission to access this resource.


Apache/2.4.38 (Debian) Server at 
www.quantum-espresso.org Port 443




From: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Ye Luo mailto:xw111lu...@gmail.com>>
Sent: Friday, February 4, 2022 12:39 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm 
OpenMPI).


export 
NETWORK_PSEUDO=http://www.quantum-espresso.org/wp-content/uploads/upf_files/
to
export 
NETWORK_PSEUDO=https://www.quantum-espresso.org/wp-content/uploads/upf_files/
in the file
ENVIRONMENT

Yes this is what I meant.  You also need to delete all the bad ones left on the 
disk from the last time.
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Re: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm OpenMPI).

[Ye Luo]

I only said edit ENVIRONMENT. The download script will add the
pseudopotential file name to NETWORK_PSEUDO and download the file.
https://www.quantum-espresso.org/wp-content/uploads/upf_files/ is not a
website.
Then `make run-tests-pw-parallel` will work.
Ye
===
Ye Luo, Ph.D.
Computational Science Division & Leadership Computing Facility
Argonne National Laboratory


On Thu, Feb 3, 2022 at 5:48 PM Husak Michal  wrote:

> Hi
>
>
> This does not work.
>
> The link bellow is not accessible in any mode ...
>
> https://www.quantum-espresso.org/wp-content/uploads/upf_files/
>
> Forbidden
>
> You don't have permission to access this resource.
>
> 
> Apache/2.4.38 (Debian) Server at www.quantum-espresso.org Port 443
>
>
>
> 
> From: users  on behalf of Ye
> Luo 
> Sent: Friday, February 4, 2022 12:39 AM
> To: Quantum ESPRESSO users Forum
> Subject: Re: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm
> OpenMPI).
>
>
> export NETWORK_PSEUDO=
> http://www.quantum-espresso.org/wp-content/uploads/upf_files/
> to
> export NETWORK_PSEUDO=
> https://www.quantum-espresso.org/wp-content/uploads/upf_files/
> in the file
> ENVIRONMENT
>
> Yes this is what I meant.  You also need to delete all the bad ones left
> on the disk from the last time.
> ___
> 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] Tracing MPI buidl of QE 7.0 malfuction (gfortranm OpenMPI).

[Husak Michal]

Hi


This does not work.

The link bellow is not accessible in any mode ...

https://www.quantum-espresso.org/wp-content/uploads/upf_files/

Forbidden

You don't have permission to access this resource.


Apache/2.4.38 (Debian) Server at www.quantum-espresso.org Port 443




From: users  on behalf of Ye Luo 

Sent: Friday, February 4, 2022 12:39 AM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm 
OpenMPI).


export 
NETWORK_PSEUDO=http://www.quantum-espresso.org/wp-content/uploads/upf_files/
to
export 
NETWORK_PSEUDO=https://www.quantum-espresso.org/wp-content/uploads/upf_files/
in the file
ENVIRONMENT

Yes this is what I meant.  You also need to delete all the bad ones left on the 
disk from the last time.
___
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users mailing list users@lists.quantum-espresso.org
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Re: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm OpenMPI).

[Ye Luo]

>
>
> export NETWORK_PSEUDO=
> http://www.quantum-espresso.org/wp-content/uploads/upf_files/
> to
> export NETWORK_PSEUDO=
> https://www.quantum-espresso.org/wp-content/uploads/upf_files/
> in the file
> ENVIRONMENT
>

Yes this is what I meant.  You also need to delete all the bad ones left on
the disk from the last time.
___
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Re: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm OpenMPI).

[Husak Michal]

Do you mean to change

export 
NETWORK_PSEUDO=http://www.quantum-espresso.org/wp-content/uploads/upf_files/
to
export 
NETWORK_PSEUDO=https://www.quantum-espresso.org/wp-content/uploads/upf_files/
in the file
ENVIRONMENT
???
This does not help ...
I was able to find most of the potencial on net, but failed with follwing one:
Download of Fe.pbe-mt_fhi.UPF FAILED, do it manually -- Testing aborted!

Michal





From: users  on behalf of Ye Luo 

Sent: Thursday, February 3, 2022 11:57 PM
To: Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm 
OpenMPI).

There was some upgrade on the server. Then curl was not happy with http. Just 
change http to https in test-suite/ENVIRONMENT.

===
Ye Luo, Ph.D.
Computational Science Division & Leadership Computing Facility
Argonne National Laboratory


On Thu, Feb 3, 2022 at 4:31 PM Husak Michal 
mailto:michal.hu...@vscht.cz>> wrote:
Hi


Thank you for your advice.

I do not thing my environment is wrong - I was able to compile similar code 
(CASTEP) with same environment 

in both MPI, and OpenMP version and it is 100% functional with all test passed 
...


I am able to build serial and OpenMP version of QE and they pass my tests, only 
OpenMPI version

fails ...

The OpenMPI fails when built from 2 totally different environments in identical 
way  = sound like no issue in my environment.


It look like current Qunatum-Espresso testsuite can not be launched,

it generate following error:

USER@USER-PC /cygdrive/m/My_project/fortran/qe/qe-7.0/test-suite
$ make run-tests
Download of O.pz-rrkjus.UPF FAILED, do it manually -- Testing aborted!
make: *** [Makefile:35: pseudo] Error 255


Sound like the server with pseudopotential is down (I am fully connected - no 
block).


Any more advice is strongly appreciated ...


Michal Husak




From: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Husak Michal mailto:michal.hu...@vscht.cz>>
Sent: Thursday, February 3, 2022 10:26 PM
To: Quantum ESPRESSO users Forum
Subject: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm OpenMPI).

Hi

I am trying to find why the MPI build (gfortan + OpenMP) does not work for QE 
6.6-7.0
The code stops in the routine
good_fft_order (in fft_support.f90)
on following statement
 IF (np <= 0 .OR. np > nr) & 

This is called from
realspace_grid_init (in fft_types.f90) ...

Following command generate nonsense input generating code stop (np=2,nr=1)
 dfft%nr1 = good_fft_order( dfft%nr1, fft_fact(1)

I am not an Fortran expert not familiar with the QE architecture so tracing 
this issue more deeply is
behind my knowledge 

Any advice I can try ?
Run some test, debug mode ?

Michal Husak
UCT Prague ...








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Re: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm OpenMPI).

[Ye Luo]

There was some upgrade on the server. Then curl was not happy with http.
Just change http to https in test-suite/ENVIRONMENT.

===
Ye Luo, Ph.D.
Computational Science Division & Leadership Computing Facility
Argonne National Laboratory


On Thu, Feb 3, 2022 at 4:31 PM Husak Michal  wrote:

> Hi
>
>
> Thank you for your advice.
>
> I do not thing my environment is wrong - I was able to compile similar
> code (CASTEP) with same environment 
>
> in both MPI, and OpenMP version and it is 100% functional with all test
> passed ...
>
>
> I am able to build serial and OpenMP version of QE and they pass my tests,
> only OpenMPI version
>
> fails ...
>
> The OpenMPI fails when built from 2 totally different environments in
> identical way  = sound like no issue in my environment.
>
>
> It look like current Qunatum-Espresso testsuite can not be launched,
>
> it generate following error:
>
> USER@USER-PC /cygdrive/m/My_project/fortran/qe/qe-7.0/test-suite
> $ make run-tests
> Download of O.pz-rrkjus.UPF FAILED, do it manually -- Testing aborted!
> make: *** [Makefile:35: pseudo] Error 255
>
>
> Sound like the server with pseudopotential is down (I am fully connected -
> no block).
>
>
> Any more advice is strongly appreciated ...
>
>
> Michal Husak
>
>
>
> 
> From: users  on behalf of Husak
> Michal 
> Sent: Thursday, February 3, 2022 10:26 PM
> To: Quantum ESPRESSO users Forum
> Subject: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm
> OpenMPI).
>
> Hi
>
> I am trying to find why the MPI build (gfortan + OpenMP) does not work for
> QE 6.6-7.0
> The code stops in the routine
> good_fft_order (in fft_support.f90)
> on following statement
>  IF (np <= 0 .OR. np > nr) & 
>
> This is called from
> realspace_grid_init (in fft_types.f90) ...
>
> Following command generate nonsense input generating code stop (np=2,nr=1)
>  dfft%nr1 = good_fft_order( dfft%nr1, fft_fact(1)
>
> I am not an Fortran expert not familiar with the QE architecture so
> tracing this issue more deeply is
> behind my knowledge 
>
> Any advice I can try ?
> Run some test, debug mode ?
>
> Michal Husak
> UCT Prague ...
>
>
>
>
>
>
>
>
> ___
> Quantum ESPRESSO is supported by MaX (www.max-centre.eu<
> http://www.max-centre.eu>)
> users mailing list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
> ___
> 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
>
___
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] Tracing MPI buidl of QE 7.0 malfuction (gfortranm OpenMPI).

[Husak Michal]

Hi


Thank you for your advice.

I do not thing my environment is wrong - I was able to compile similar code 
(CASTEP) with same environment 

in both MPI, and OpenMP version and it is 100% functional with all test passed 
...


I am able to build serial and OpenMP version of QE and they pass my tests, only 
OpenMPI version

fails ...

The OpenMPI fails when built from 2 totally different environments in identical 
way  = sound like no issue in my environment.


It look like current Qunatum-Espresso testsuite can not be launched,

it generate following error:

USER@USER-PC /cygdrive/m/My_project/fortran/qe/qe-7.0/test-suite
$ make run-tests
Download of O.pz-rrkjus.UPF FAILED, do it manually -- Testing aborted!
make: *** [Makefile:35: pseudo] Error 255


Sound like the server with pseudopotential is down (I am fully connected - no 
block).


Any more advice is strongly appreciated ...


Michal Husak




From: users  on behalf of Husak 
Michal 
Sent: Thursday, February 3, 2022 10:26 PM
To: Quantum ESPRESSO users Forum
Subject: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm OpenMPI).

Hi

I am trying to find why the MPI build (gfortan + OpenMP) does not work for QE 
6.6-7.0
The code stops in the routine
good_fft_order (in fft_support.f90)
on following statement
 IF (np <= 0 .OR. np > nr) & 

This is called from
realspace_grid_init (in fft_types.f90) ...

Following command generate nonsense input generating code stop (np=2,nr=1)
 dfft%nr1 = good_fft_order( dfft%nr1, fft_fact(1)

I am not an Fortran expert not familiar with the QE architecture so tracing 
this issue more deeply is
behind my knowledge 

Any advice I can try ?
Run some test, debug mode ?

Michal Husak
UCT Prague ...








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Re: [QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm OpenMPI).

[Ye Luo]

build QE without MPI without OpenMP, run test-suite. To check if your
compiler and library works.
build QE with MPI without OpenMP, run test-suite. To check if your MPI
library works properly.
build QE without MPI but with OpenMP, run test-suite. To check if OpenMP is
the issue.
build QE with MPI and with OpenMP, run test-suite. To check if OpenMP+MPI
works.
If any of the above case shows massive failure, you'd better check the
software environment. I think this is likely the case.
If all the above cases pass, but your own tests fail. Provide a full
reproducer (how you build the code, all the input/output/log of run)
Ye
===
Ye Luo, Ph.D.
Computational Science Division & Leadership Computing Facility
Argonne National Laboratory


On Thu, Feb 3, 2022 at 3:27 PM Husak Michal  wrote:

> Hi
>
> I am trying to find why the MPI build (gfortan + OpenMP) does not work for
> QE 6.6-7.0
> The code stops in the routine
> good_fft_order (in fft_support.f90)
> on following statement
>  IF (np <= 0 .OR. np > nr) & 
>
> This is called from
> realspace_grid_init (in fft_types.f90) ...
>
> Following command generate nonsense input generating code stop (np=2,nr=1)
>  dfft%nr1 = good_fft_order( dfft%nr1, fft_fact(1)
>
> I am not an Fortran expert not familiar with the QE architecture so
> tracing this issue more deeply is
> behind my knowledge 
>
> Any advice I can try ?
> Run some test, debug mode ?
>
> Michal Husak
> UCT Prague ...
>
>
>
>
>
>
>
>
> ___
> 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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[QE-users] Tracing MPI buidl of QE 7.0 malfuction (gfortranm OpenMPI).

[Husak Michal]

Hi

I am trying to find why the MPI build (gfortan + OpenMP) does not work for QE 
6.6-7.0
The code stops in the routine
good_fft_order (in fft_support.f90)
on following statement
 IF (np <= 0 .OR. np > nr) & 

This is called from
realspace_grid_init (in fft_types.f90) ...

Following command generate nonsense input generating code stop (np=2,nr=1)
 dfft%nr1 = good_fft_order( dfft%nr1, fft_fact(1)

I am not an Fortran expert not familiar with the QE architecture so tracing 
this issue more deeply is
behind my knowledge 

Any advice I can try ?
Run some test, debug mode ?

Michal Husak
UCT Prague ...








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[QE-users] Changing masses of a dynamical matrix

[Antoine Jay]

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

[Vivek Christhunathan]

Hi Lorenzo,

Thank you very much for your response.

Sorry for the earlier message. I did not get notified on this.

>$ ~/espresso.BASE/PW/tools/scan_ibrav.x

Yes, I will get used to it on this.

As per your suggestion, I will use the following values for my calculation
and let you know the results.

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


Thanks a million.

Kind Regards,

Vivek C


__

Vivek Christhunathan

PhD researcher

Mechanical Engineering

College of Engineering and Informatics

Room 2053

Alice Perry Engineering Building

National University of Ireland Galway

Ireland
E-mail: v.christhunath...@nuigalway.ie
Phone: +353 899811181, +91 9600752742



On Thu, Feb 3, 2022 at 2:05 PM Vivek Christhunathan 
wrote:

> Hello Everyone,
>
> I could not solve this issue even after trying with v6.8 (the older
> version was v6.4.1). Still, the CaWO4 (2x1x1 supercell) changes its
> symmetry from Tetragonal to Orthorhombic while doing structural
> relaxation. Even I tried with multiple different input parameters.
>
> Can I get any suggestions regarding this, please?
>
> Kind Regards,
>
> Vivek C
>
>
> __
>
> Vivek Christhunathan
>
> PhD researcher
>
> Mechanical Engineering
>
> College of Engineering and Informatics
>
> Room 2053
>
> Alice Perry Engineering Building
>
> National University of Ireland Galway
>
> Ireland
> E-mail: v.christhunath...@nuigalway.ie
> Phone: +353 899811181, +91 9600752742
>
>
>
> On Tue, Feb 1, 2022 at 12:52 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:
>> filebackports-6.4.1.diff*
>>
>> 
>> in https://github.com/QEF/q-e/releases
>>
>>
>> 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:*
>>
>> &control
>> 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,
>> /
>>
>> &system
>> ibrav = 0
>> *celldm(1) = 19.820415*
>> nat = 48
>> ntyp = 3
>> ecutwfc = 65.0
>> ecutrho = 780.0
>> occupations= 'smearing'
>> smearing= 'gaussian'
>> degauss= 0.02
>> /
>>
>> &electrons
>> mixing_beta = 0.2,
>> conv_thr = 1.0d-6,
>> electron_maxstep = 5,
>> /
>>
>> &IONS
>> *ion_dynamics = 'damp'*
>>
>> /
>>
>> &cell
>> cell_factor = 3.0d0
>> *cell_dynamics = 'damp-pr'*
>> !cell_dofree= 'ibrav'
>> /
>>
>> ATOMIC_SPECIES
>>  Ca 40.08   Ca.pbe-spn-rrkjus_psl.1.0.0.UPF
>>  W  183.84  W.pbe-spn-rrkjus_psl.1.0.0.UPF
>>  O  16.00   O.pbe-n-rrkjus_psl.1.0.0.UPF
>>
>> *CELL_PARAMETERS (alat)*
>> *1.00 0.00 0.00*
>> *0.00 0.49 0.00*
>> *0.00 0.00 1.0845493931*
>>
>> ATOMIC_POSITIONS (crystal)
>> Ca 0.0 0.25000 0.62500
>> Ca 0.5 0.25000 0.62500
>> Ca 0.0 0.75000 0.37500
>> Ca 0.5 0.75000 0.37500
>> Ca 0.25000 0.75000 0.12500
>> Ca 0.75000 0.75000 0.12500
>> Ca 0.25000 0.25000 0.87500
>> Ca 0.75000 0.25000

Re: [QE-users] Reconstruction problem in hp.x :Error in routine reconstruct_full_chi (1)

[Vahid Askarpour]

Dear Iurii,

Thank you for the clarification and the reference. It seems that I have much to 
learn.

Cheers,
Vahid

On Feb 3, 2022, at 10:13 AM, Iurii TIMROV 
mailto:iurii.tim...@epfl.ch>> wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Vahid,

> I am getting large U parameters (~60 and 20eV) for the two species and am 
> trying to figure out if these values are realistic or not.

They are not!

For closed-shell systems the U value is unphysically large: K. Yu and E.A. 
Carter, J. Chem. Phys. 140, 121105 (2014).
This is a well-known limitation of the current method to determine U.

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

From: Vahid Askarpour mailto:vh261...@dal.ca>>
Sent: Thursday, February 3, 2022 2:57:07 PM
To: Iurii TIMROV; Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Reconstruction problem in hp.x :Error in routine 
reconstruct_full_chi (1)

Hi Iurii and Iman,

I tried  your second test (the first test failed) using find_atpert=1 and 
docc_thr=1.D-15 in my input and the hp.x code perturbed all atoms and the 
reconstruction error was avoided. I am getting large U parameters (~60 and 
20eV) for the two species and am trying to figure out if these values are 
realistic or not. The new bandgap is ~ 9eV but I was expecting around 3-4eV. 
The U=0 gap is ~2eV.

Cheers,
Vahid

On Feb 3, 2022, at 9:13 AM, Iurii TIMROV via users 
mailto:users@lists.quantum-espresso.org>> 
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Iman Bezzaoui,

Please remember to sign your posts.

We cannot help if you do not provide enough details about your calculations (QE 
version, input and output files, etc.).

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 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Bezzaoui Iman 
mailto:imanbezza...@gmail.com>>
Sent: Thursday, February 3, 2022 1:38:08 PM
To: users@lists.quantum-espresso.org
Subject: [QE-users] Reconstruction problem in hp.x :Error in routine 
reconstruct_full_chi (1)

I’m using DFT+U+V calculation, to calculate the U_Hubbard parameter and 
V_Hubbard parameter.
I relaxed the symmetry slab of 34 atoms then I'm running SCF calculation but 
when I’m running in hp.x I find this :
Missing chi element for: na=32  nb=19  dist=   6.103609


 Missing chi element for: na=32  nb=22  dist=   6.154417


 Missing chi element for: na=32  nb=34  dist=   9.335406


 Missing chi element for: na=34  nb=20  dist=   8.721532


 Missing chi element for: na=34  nb=23  dist=  10.355784


 Missing chi element for: na=34  nb=24  dist=  10.355784


 Missing chi element for: na=34  nb=30  dist=   9.947637


 Missing chi element for: na=34  nb=32  dist=   9.335406


%%
 Error in routine reconstruct_full_chi (1):
 Reconstruction problem: some chi were not found
%%


[https://lh3.googleusercontent.com/a-/AOh14GgK3_3VvG6N0BAvJU0qYserAnBe2FiHuKliKV-t=s40]
RépondreTransférer
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Re: [QE-users] Reconstruction problem in hp.x :Error in routine reconstruct_full_chi (1)

[Iurii TIMROV via users]

Dear Vahid,


> I am getting large U parameters (~60 and 20eV) for the two species and am 
> trying to figure out if these values are realistic or not.


They are not!


For closed-shell systems the U value is unphysically large: K. Yu and E.A. 
Carter, J. Chem. Phys. 140, 121105 (2014).

This is a well-known limitation of the current method to determine U.


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

From: Vahid Askarpour 
Sent: Thursday, February 3, 2022 2:57:07 PM
To: Iurii TIMROV; Quantum ESPRESSO users Forum
Subject: Re: [QE-users] Reconstruction problem in hp.x :Error in routine 
reconstruct_full_chi (1)

Hi Iurii and Iman,

I tried  your second test (the first test failed) using find_atpert=1 and 
docc_thr=1.D-15 in my input and the hp.x code perturbed all atoms and the 
reconstruction error was avoided. I am getting large U parameters (~60 and 
20eV) for the two species and am trying to figure out if these values are 
realistic or not. The new bandgap is ~ 9eV but I was expecting around 3-4eV. 
The U=0 gap is ~2eV.

Cheers,
Vahid

On Feb 3, 2022, at 9:13 AM, Iurii TIMROV via users 
mailto:users@lists.quantum-espresso.org>> 
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.



Dear Iman Bezzaoui,

Please remember to sign your posts.

We cannot help if you do not provide enough details about your calculations (QE 
version, input and output files, etc.).

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 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Bezzaoui Iman 
mailto:imanbezza...@gmail.com>>
Sent: Thursday, February 3, 2022 1:38:08 PM
To: users@lists.quantum-espresso.org
Subject: [QE-users] Reconstruction problem in hp.x :Error in routine 
reconstruct_full_chi (1)

I’m using DFT+U+V calculation, to calculate the U_Hubbard parameter and 
V_Hubbard parameter.
I relaxed the symmetry slab of 34 atoms then I'm running SCF calculation but 
when I’m running in hp.x I find this :
Missing chi element for: na=32  nb=19  dist=   6.103609


 Missing chi element for: na=32  nb=22  dist=   6.154417


 Missing chi element for: na=32  nb=34  dist=   9.335406


 Missing chi element for: na=34  nb=20  dist=   8.721532


 Missing chi element for: na=34  nb=23  dist=  10.355784


 Missing chi element for: na=34  nb=24  dist=  10.355784


 Missing chi element for: na=34  nb=30  dist=   9.947637


 Missing chi element for: na=34  nb=32  dist=   9.335406


%%
 Error in routine reconstruct_full_chi (1):
 Reconstruction problem: some chi were not found
%%


[https://lh3.googleusercontent.com/a-/AOh14GgK3_3VvG6N0BAvJU0qYserAnBe2FiHuKliKV-t=s40]
RépondreTransférer

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users@lists.quantum-espresso.org
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Re: [QE-users] Crystal structure changes while doing vc-relax calculation.

[Vivek Christhunathan]

Hello Everyone,

I could not solve this issue even after trying with v6.8 (the older version
was v6.4.1). Still, the CaWO4 (2x1x1 supercell) changes its symmetry
from Tetragonal
to Orthorhombic while doing structural relaxation. Even I tried with
multiple different input parameters.

Can I get any suggestions regarding this, please?

Kind Regards,

Vivek C


__

Vivek Christhunathan

PhD researcher

Mechanical Engineering

College of Engineering and Informatics

Room 2053

Alice Perry Engineering Building

National University of Ireland Galway

Ireland
E-mail: v.christhunath...@nuigalway.ie
Phone: +353 899811181, +91 9600752742



On Tue, Feb 1, 2022 at 12:52 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:
> filebackports-6.4.1.diff*
>
> 
> in https://github.com/QEF/q-e/releases
>
>
> 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:*
>
> &control
> 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,
> /
>
> &system
> ibrav = 0
> *celldm(1) = 19.820415*
> nat = 48
> ntyp = 3
> ecutwfc = 65.0
> ecutrho = 780.0
> occupations= 'smearing'
> smearing= 'gaussian'
> degauss= 0.02
> /
>
> &electrons
> mixing_beta = 0.2,
> conv_thr = 1.0d-6,
> electron_maxstep = 5,
> /
>
> &IONS
> *ion_dynamics = 'damp'*
>
> /
>
> &cell
> cell_factor = 3.0d0
> *cell_dynamics = 'damp-pr'*
> !cell_dofree= 'ibrav'
> /
>
> ATOMIC_SPECIES
>  Ca 40.08   Ca.pbe-spn-rrkjus_psl.1.0.0.UPF
>  W  183.84  W.pbe-spn-rrkjus_psl.1.0.0.UPF
>  O  16.00   O.pbe-n-rrkjus_psl.1.0.0.UPF
>
> *CELL_PARAMETERS (alat)*
> *1.00 0.00 0.00*
> *0.00 0.49 0.00*
> *0.00 0.00 1.0845493931*
>
> ATOMIC_POSITIONS (crystal)
> Ca 0.0 0.25000 0.62500
> Ca 0.5 0.25000 0.62500
> Ca 0.0 0.75000 0.37500
> Ca 0.5 0.75000 0.37500
> Ca 0.25000 0.75000 0.12500
> Ca 0.75000 0.75000 0.12500
> Ca 0.25000 0.25000 0.87500
> Ca 0.75000 0.25000 0.87500
>  W 0.0 0.25000 0.12500
>  W 0.5 0.25000 0.12500
>  W 0.0 0.75000 0.87500
>  W 0.5 0.75000 0.87500
>  W 0.25000 0.75000 0.62500
>  W 0.75000 0.75000 0.62500
>  W 0.25000 0.25000 0.37500
>  W 0.75000 0.25000 0.37500
>  O 0.07485 0.00930 0.20973
>  O 0.574850023 0.00930 0.20973
>  O 0.425150007 0.99076 0.790300012
>  O 0.925150037 0.99076 0.790300012
>  O 0.175150007 0.99076 0.709699988
>  O 0.675150037 0.99076 0.709699988
>  O 0.324849993 0.00930 0.290300012
>  O 0.824849963 0.00930 0.290300012
>  O 0.370350003 0.399699986 0.459699988
>  O 0.87035000

Re: [QE-users] Reconstruction problem in hp.x :Error in routine reconstruct_full_chi (1)

[Vahid Askarpour]

Hi Iurii and Iman,

I tried  your second test (the first test failed) using find_atpert=1 and 
docc_thr=1.D-15 in my input and the hp.x code perturbed all atoms and the 
reconstruction error was avoided. I am getting large U parameters (~60 and 
20eV) for the two species and am trying to figure out if these values are 
realistic or not. The new bandgap is ~ 9eV but I was expecting around 3-4eV. 
The U=0 gap is ~2eV.

Cheers,
Vahid

On Feb 3, 2022, at 9:13 AM, Iurii TIMROV via users 
mailto:users@lists.quantum-espresso.org>> 
wrote:

CAUTION: The Sender of this email is not from within Dalhousie.
Dear Iman Bezzaoui,

Please remember to sign your posts.

We cannot help if you do not provide enough details about your calculations (QE 
version, input and output files, etc.).

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 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Bezzaoui Iman 
mailto:imanbezza...@gmail.com>>
Sent: Thursday, February 3, 2022 1:38:08 PM
To: users@lists.quantum-espresso.org
Subject: [QE-users] Reconstruction problem in hp.x :Error in routine 
reconstruct_full_chi (1)

I’m using DFT+U+V calculation, to calculate the U_Hubbard parameter and 
V_Hubbard parameter.
I relaxed the symmetry slab of 34 atoms then I'm running SCF calculation but 
when I’m running in hp.x I find this :
Missing chi element for: na=32  nb=19  dist=   6.103609


 Missing chi element for: na=32  nb=22  dist=   6.154417


 Missing chi element for: na=32  nb=34  dist=   9.335406


 Missing chi element for: na=34  nb=20  dist=   8.721532


 Missing chi element for: na=34  nb=23  dist=  10.355784


 Missing chi element for: na=34  nb=24  dist=  10.355784


 Missing chi element for: na=34  nb=30  dist=   9.947637


 Missing chi element for: na=34  nb=32  dist=   9.335406


%%
 Error in routine reconstruct_full_chi (1):
 Reconstruction problem: some chi were not found
%%


[https://lh3.googleusercontent.com/a-/AOh14GgK3_3VvG6N0BAvJU0qYserAnBe2FiHuKliKV-t=s40]
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Re: [QE-users] Reconstruction problem in hp.x :Error in routine reconstruct_full_chi (1)

[Iurii TIMROV via users]

Dear Iman Bezzaoui,


Please remember to sign your posts.


We cannot help if you do not provide enough details about your calculations (QE 
version, input and output files, etc.).


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 Bezzaoui 
Iman 
Sent: Thursday, February 3, 2022 1:38:08 PM
To: users@lists.quantum-espresso.org
Subject: [QE-users] Reconstruction problem in hp.x :Error in routine 
reconstruct_full_chi (1)

I’m using DFT+U+V calculation, to calculate the U_Hubbard parameter and 
V_Hubbard parameter.
I relaxed the symmetry slab of 34 atoms then I'm running SCF calculation but 
when I’m running in hp.x I find this :
Missing chi element for: na=32  nb=19  dist=   6.103609


 Missing chi element for: na=32  nb=22  dist=   6.154417


 Missing chi element for: na=32  nb=34  dist=   9.335406


 Missing chi element for: na=34  nb=20  dist=   8.721532


 Missing chi element for: na=34  nb=23  dist=  10.355784


 Missing chi element for: na=34  nb=24  dist=  10.355784


 Missing chi element for: na=34  nb=30  dist=   9.947637


 Missing chi element for: na=34  nb=32  dist=   9.335406


%%
 Error in routine reconstruct_full_chi (1):
 Reconstruction problem: some chi were not found
%%


[https://lh3.googleusercontent.com/a-/AOh14GgK3_3VvG6N0BAvJU0qYserAnBe2FiHuKliKV-t=s40]
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[QE-users] Reconstruction problem in hp.x :Error in routine reconstruct_full_chi (1)

[Bezzaoui Iman]

I’m using DFT+U+V calculation, to calculate the U_Hubbard parameter and
V_Hubbard parameter.

I relaxed the symmetry slab of 34 atoms then I'm running SCF calculation
but when I’m running in hp.x I find this :

Missing chi element for: na=32  nb=19  dist=   6.103609





 Missing chi element for: na=32  nb=22  dist=   6.154417





 Missing chi element for: na=32  nb=34  dist=   9.335406





 Missing chi element for: na=34  nb=20  dist=   8.721532





 Missing chi element for: na=34  nb=23  dist=  10.355784





 Missing chi element for: na=34  nb=24  dist=  10.355784





 Missing chi element for: na=34  nb=30  dist=   9.947637





 Missing chi element for: na=34  nb=32  dist=   9.335406





%%

 Error in routine reconstruct_full_chi (1):

 Reconstruction problem: some chi were not found

%%




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Re: [QE-users] Different phonon frequencies at Gamma point via q2r.x + dynmat.x and matdyn.x calculation.

[zhishuohuang]

Dear Prof. Giannozzi,

 

Thank you for your explanation.

 

Best regards

Zhishuo Huang

 

From: Paolo Giannozzi  
Sent: Thursday, February 3, 2022 6:09 PM
To: Quantum ESPRESSO users Forum 
Cc: 黄志硕 
Subject: Re: [QE-users] Different phonon frequencies at Gamma point via q2r.x + 
dynmat.x and matdyn.x calculation.

 

On Thu, Feb 3, 2022 at 10:44 AM mailto:zhishuohu...@gmail.com> > wrote:

 

 A direction for q was not specified:TO-LO splitting will be absent

 

This explains the "discrepancy"


 

Paol

-- 

Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222

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Re: [QE-users] Different phonon frequencies at Gamma point via q2r.x + dynmat.x and matdyn.x calculation.

[Paolo Giannozzi]

On Thu, Feb 3, 2022 at 10:44 AM  wrote:

 A direction for q was not specified:TO-LO splitting will be absent
>

This explains the "discrepancy"

Paol
-- 
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 206, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
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[QE-users] Different phonon frequencies at Gamma point via q2r.x + dynmat.x and matdyn.x calculation.

[zhishuohuang]

Dear all,

 

I encountered one problem when doing phonon calculations. 

 

I tried to do the test calculation provided in the
'qe-6.8/PHonon/examples/GRID_example'. 

After the whole calculations finished, the phonon frequencies of Gamma point
are shown below:

###

&plot nbnd=   6, nks= 161 /

0.00  0.00  0.00

   -0.   -0.   -0.  375.5206  375.5206  410.5615

.

.

###

 

The input file is 

###

&input

  asr='simple',

  flfrc='AlAs.fc',

  flfrq='AlAs.freq',

  flvec='AlAs.modes',

  q_in_band_form=.true.,

  amass(1)=26.98,

  amass(2)=74.92,

/

6

  0.000 0.0 0.0   40

  1.0   0.0 0.0   20

  1.0   0.5 0.0   20

  1.0   1.0 0.0   40

  0.00  0.0 0.0   40

  0.5   0.5 0.51

###

 

 

However, if I used the first dynamic matrix, which corresponds to that of
Gamma point, and do phonon calculation for Gamma point via dynmat.x with the
input file:

###

&input

fildyn='AlAs.dynG', asr='simple',

fileig='AlAs.eigfile', filout='AlAs.normal'

amass(1)=26.98,

amass(2)=74.92,

/

###

 

The output file is 

###

 Program DYNMAT v.6.8 starts on  3Feb2022 at 16:54:12

 

 This program is part of the open-source Quantum ESPRESSO suite

 for quantum simulation of materials; please cite

 "P. Giannozzi et al., J. Phys.:Condens. Matter 21 395502 (2009);

 "P. Giannozzi et al., J. Phys.:Condens. Matter 29 465901 (2017);

 "P. Giannozzi et al., J. Chem. Phys. 152 154105 (2020);

  URL http://www.quantum-espresso.org";,

 in publications or presentations arising from this work. More details
at

 http://www.quantum-espresso.org/quote

 

 Parallel version (MPI & OpenMP), running on   4 processor cores

 Number of MPI processes: 4

 Threads/MPI process: 1

 

 MPI processes distributed on 1 nodes

 R & G space division:  proc/nbgrp/npool/nimage =   4

 121728 MiB available memory on the printing compute node when the
environment starts

 

 

 Reading Dynamical Matrix from file AlAs.dynG

 ...Force constants read

 ...epsilon and Z* read

 A direction for q was not specified:TO-LO splitting will be absent

 

 Polarizability (A^3 units)

 multiply by 0.190550 for Clausius-Mossotti correction

43.4913640.00   -0.00

 0.00   43.4913640.00

-0.000.00   43.491364

 

 IR activities are in (D/A)^2/amu units

 

# mode   [cm-1][THz]  IR

1 -0.00   -0.0.

2  0.000.0.

3  0.000.0.

4375.52   11.25787.6122

5375.52   11.25787.6122

6375.52   11.25787.6122

 

 DYNMAT   :  0.01s CPU  0.03s WALL

 

 

   This run was terminated on:  16:54:12   3Feb2022

 

=---
---=

   JOB DONE.

=---
---=

###

 

The highest phonon frequencies (375.52 cm $^{-1}$ vs 410.5615 cm $^{-1}$)
differ a lot. 

 

Could anyone please tell me why there is such a hug difference? And how to
eliminate the difference?

 

I also tried calculations on other materials, the single point phonon
calculation at Gamma point gives no imaginary frequencies while when doing
the full phonon dispersion calculations, there exist huge imaginary
frequencies at Gamma point. 

 

Best regards

Zhishuo Huang

 

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Re: [QE-users] problem in running pw2wannier90.x

[Soumendra Kumar Das]

Dear  Raghottam,

Thank you so much. It works now.

On Tue, Feb 1, 2022 at 11:20 AM Raghottam Sattigeri <
raghottam.s-...@msubaroda.ac.in> wrote:

> You have given both prefix and seedname and the script does not end with a
> "/". Probably this is creating the problem.
>
> On Tue, Feb 1, 2022, 10:34 Soumendra Kumar Das 
> wrote:
>
>> Dear QE users,
>>
>> I am running the wannier canculation for Bi2Se3. I have successfully run
>> scf, nscf, wannier90.x -pp. But while running pw2wannier90.x I am getting
>> this error.
>>
>>
>>
>>  
>> %%
>>  Error in routine pw2wannier90 (1):
>>  reading inputpp namelist
>>
>>  
>> %%
>>
>>  stopping ...
>>
>> Here is my input filr for pw2wan.
>>
>> &inputpp
>>   outdir =  'temp2'
>>   prefix =  'Bi2Se3'
>>   seedname   =  'wannier'
>>   write_amn  =  .true.
>>   write_mmn  =  .true.
>>   write_unk  =  .true.
>>
>>
>> Please suggest to me what I should do on this. I am using qe-6.5.
>> --
>> *---*
>> *Thanks and Regards*
>> *Soumendra Kumar Das*
>>
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-- 
*---*
*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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