Re: [QE-users] help in understand why ph.x crashes with electron_phonon = 'interpolated'

2022-05-09 Thread Paolo Giannozzi 
Have you looked at PHonon/examples/example03 and followed the procedure 
described there?


Paolo

On 09/05/2022 07:46, patrizio.grazi...@cnr.it wrote:

Hello everybody,

I'm experiencing a crash in ph.x but I cannot figure out the reason, so 
I ask you some suggestion if possible, please.


I'm working on FCC Co with q-e/7.0 on CINECA cluster, if I use the 
following input file without the line electron_phonon = 'interpolated', 
it runs smoothly, but with the electron_phonon spec it crashes.



   verbosity='debug'
   tr2_ph=1.0d-17
   prefix='Co'
   ldisp=.true.
   epsil=.false.
   lqdir=.true.
   outdir='./tmp'
   fildyn='Co.dyn'
   fildvscf = 'dvscf'
   electron_phonon = 'interpolated'
   nq1=10, nq2=10, nq3=10,
   !nk1=20, nk2=20, nk3=20
/



In the output file (attached) it looks the code runs until the following 
point, which looks the first e-ph calc.


Number of q in the star =    1
  List of q in the star:
   1   0.0   0.0   0.0

  Diagonalizing the dynamical matrix

  q = (    0.0   0.0   0.0 )

  **
  freq (    1) =   0.782369 [THz] =  26.097029 [cm-1]
  freq (    2) =   0.782369 [THz] =  26.097029 [cm-1]
  freq (    3) =   0.782369 [THz] =  26.097029 [cm-1]
  **

  Mode symmetry, O_h (m-3m)  point group:

  freq (   1-   3) = 26.1  [cm-1]   --> T_1u G_15  G_4- I
  electron-phonon interaction  ...




and in the output file of the run, I see a bunch of lines like the 
following


forrtl: severe (24): end-of-file during read, unit 40, file 
/g100_scratch/userexternal/pgrazios/MatrixElements/Co_interp_fcc/./tmp/Co.a2Fsave 


Image  PC    Routine    Line    Source
ph.x   00FECD08  Unknown   Unknown  Unknown
ph.x   01027ECA  Unknown   Unknown  Unknown
ph.x   004339EC  elphsum_  842  
elphon.f90
ph.x   0040D3A6  do_phonon_    143  
do_phonon.f90
ph.x   0040754B  MAIN__ 78  
phonon.f90

ph.x   004074A2  Unknown   Unknown  Unknown
libc-2.28.so   147385E7E493  __libc_start_main Unknown  Unknown
ph.x   004073AE  Unknown   Unknown  Unknown
srun: error: r501n013: task 0: Exited with exit code 24
srun: launch/slurm: _step_signal: Terminating StepId=3470527.0
slurmstepd: error: *** STEP 3470527.0 ON r501n013 CANCELLED AT 
2022-05-07T07:34:27 ***

forrtl: error (78): process killed (SIGTERM)
Image  PC    Routine    Line    Source
ph.x   00FFBB1B  Unknown   Unknown  Unknown
libpthread-2.28.s  14B7002C3B20  Unknown   Unknown  Unknown
libmpi.so.12.0.0   14B700B10D6B  Unknown   Unknown  Unknown
libmpi.so.12.0.0   14B700B04F87  Unknown   Unknown  Unknown
libmpi.so.12.0.0   14B700A806C3  Unknown   Unknown  Unknown
libmpi.so.12.0.0   14B700A57C51  Unknown   Unknown  Unknown
libmpi.so.12.0.0   14B700A3BACA  Unknown   Unknown  Unknown
libmpi.so.12.0.0   14B700B1EDE5  Unknown   Unknown  Unknown
libmpi.so.12.0.0   14B700A1AD6D  MPI_Barrier   Unknown  Unknown
libmpifort.so.12.  14B701DBC7BC  pmpi_barrier  Unknown  Unknown
ph.x   00DF3B97  bcast_integer_ 60  
mp_base.f90

ph.x   00DD22E8  mp_mp_mp_bcast_i1 443  mp.f90
ph.x   0042AD26  elphsum_  845  
elphon.f90
ph.x   0040D3A6  do_phonon_    143  
do_phonon.f90
ph.x   0040754B  MAIN__ 78  
phonon.f90

ph.x   004074A2  Unknown   Unknown  Unknown
libc-2.28.so   14B6FF76D493  __libc_start_main Unknown  Unknown
ph.x   004073AE  Unknown   Unknown  Unknown
forrtl: error (78): process killed (SIGTERM)



The previous scf calc. has been done with PBE pseudopotential without 
spin orbit.


Can you give me some hints on how to fix the problem, please?

Thanks
Patrizio


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--

Re: [QE-users] PWSCF v.7.0 unknown vdw correction (vdw_corr): mbd_vdw.

2022-05-09 Thread Hsin-Yu Ko 
Thanks, Paolo! I also submitted a quick patch to the Gitlab repo for your 
consideration.

--
Hsin-Yu Ko
Postdoctoral Research Fellow
Department of Chemistry and Chemical Biology
Cornell University


From: Paolo Giannozzi 
Sent: Monday, May 9, 2022 9:42 AM
To: users@lists.quantum-espresso.org 
Cc: Hsin-Yu Ko 
Subject: Re: [QE-users] PWSCF v.7.0 unknown vdw correction (vdw_corr): mbd_vdw.

On 09/05/2022 14:15, Hsin-Yu Ko wrote:

> Please try vdw_corr = 'mbd' instead, and I will check if the
> documentation in the development version has been fixed.

the documentation is still incomplete and lists 'mbd_vdw' and 'many-body
dispersion' as only possibilities, but the code had been meanwhile fixed
and it recognizes both now:

$ grep MBD q-e-dev/Modules/set_vdw_corr.f90
   CASE( 'MBD', 'mbd', 'many-body-dispersion', 'mbd_vdw' )

Paolo

>
> Thank you,
> Hsin-Yu
>
> --
> Hsin-Yu Ko
> Postdoctoral Research Fellow
> Department of Chemistry and Chemical Biology
> Cornell University
>
> 
> *From:* users  on behalf of
> Stoppelman, John P 
> *Sent:* Monday, May 9, 2022 7:38 AM
> *To:* users@lists.quantum-espresso.org 
> *Subject:* [QE-users] PWSCF v.7.0 unknown vdw correction (vdw_corr):
> mbd_vdw.
>
> Hello,
>
> I downloaded and compiled Quantum Espresso 7.0 from
> https://www.quantum-espresso.org/download-page/
>  and compiled using
> ‘./configure’ and ‘make all’. When I include the option:
>
> vdw_corr = 'mbd_vdw'
>
> in my input file for pw.x I get the warning:
>
>   Message from routine set_vdw_corr:
>
>   WARNING: unknown vdw correction (vdw_corr): mbd_vdw. No vdw
> correction used.
>
> Is there something I’m missing for compiling libmbd with Quantum
> Espresso? I see ‘make’ does create a directory in qe-7.0 called MBD
> which seems to contain the source code for libmbd. Is there any other
> step I need to take? My linux OS is RHEL 7.9 for reference.
>
> Thanks for any potential help,
>
> John Stoppelman
>
>
> ___
> 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 list users@lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users

--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
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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Re: [QE-users] PWSCF v.7.0 unknown vdw correction (vdw_corr): mbd_vdw.

2022-05-09 Thread Paolo Giannozzi 

On 09/05/2022 14:15, Hsin-Yu Ko wrote:

Please try vdw_corr = 'mbd' instead, and I will check if the 
documentation in the development version has been fixed.


the documentation is still incomplete and lists 'mbd_vdw' and 'many-body 
dispersion' as only possibilities, but the code had been meanwhile fixed 
and it recognizes both now:


$ grep MBD q-e-dev/Modules/set_vdw_corr.f90
  CASE( 'MBD', 'mbd', 'many-body-dispersion', 'mbd_vdw' )

Paolo



Thank you,
Hsin-Yu

--
Hsin-Yu Ko
Postdoctoral Research Fellow
Department of Chemistry and Chemical Biology
Cornell University


*From:* users  on behalf of 
Stoppelman, John P 

*Sent:* Monday, May 9, 2022 7:38 AM
*To:* users@lists.quantum-espresso.org 
*Subject:* [QE-users] PWSCF v.7.0 unknown vdw correction (vdw_corr): 
mbd_vdw.


Hello,

I downloaded and compiled Quantum Espresso 7.0 from 
https://www.quantum-espresso.org/download-page/ 
 and compiled using 
‘./configure’ and ‘make all’. When I include the option:


vdw_corr = 'mbd_vdw'

in my input file for pw.x I get the warning:

  Message from routine set_vdw_corr:

  WARNING: unknown vdw correction (vdw_corr): mbd_vdw. No vdw 
correction used.


Is there something I’m missing for compiling libmbd with Quantum 
Espresso? I see ‘make’ does create a directory in qe-7.0 called MBD 
which seems to contain the source code for libmbd. Is there any other 
step I need to take? My linux OS is RHEL 7.9 for reference.


Thanks for any potential help,

John Stoppelman


___
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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--
Paolo Giannozzi, Dip. Scienze Matematiche Informatiche e Fisiche,
Univ. Udine, via delle Scienze 208, 33100 Udine, Italy
Phone +39-0432-558216, fax +39-0432-558222
___
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 list users@lists.quantum-espresso.org
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Re: [QE-users] PWSCF v.7.0 unknown vdw correction (vdw_corr): mbd_vdw.

2022-05-09 Thread Stoppelman, John P 
Hello,
Yes, that seems to be the fix. Thank you for the help!
From,
John Stoppelman

From: users  On Behalf Of Hsin-Yu Ko
Sent: Monday, May 9, 2022 8:16 AM
To: users@lists.quantum-espresso.org
Subject: Re: [QE-users] PWSCF v.7.0 unknown vdw correction (vdw_corr): mbd_vdw.

Hi John,

Somehow the documentation is inconsistent with the source code. I did a quick 
search in `Modules/set_vdw_corr.f90` and found the following:
```
$ grep -n -C 3 MBD Modules/set_vdw_corr.f90
30-  CASE( 'TS', 'ts', 'ts-vdw', 'ts-vdW', 'tkatchenko-scheffler' )
31- ts_vdw = .TRUE.
32-
33:  CASE( 'MBD', 'mbd', 'many-body-dispersion' )
34- ts_vdw = .TRUE.
35- mbd_vdw = .TRUE.
36-
```

Please try vdw_corr = 'mbd' instead, and I will check if the documentation in 
the development version has been fixed.

Thank you,
Hsin-Yu

--
Hsin-Yu Ko
Postdoctoral Research Fellow
Department of Chemistry and Chemical Biology
Cornell University


From: users 
mailto:users-boun...@lists.quantum-espresso.org>>
 on behalf of Stoppelman, John P 
mailto:jstoppelm...@gatech.edu>>
Sent: Monday, May 9, 2022 7:38 AM
To: users@lists.quantum-espresso.org 
mailto:users@lists.quantum-espresso.org>>
Subject: [QE-users] PWSCF v.7.0 unknown vdw correction (vdw_corr): mbd_vdw.


Hello,

I downloaded and compiled Quantum Espresso 7.0 from 
https://www.quantum-espresso.org/download-page/ and compiled using 
'./configure' and 'make all'. When I include the option:



vdw_corr = 'mbd_vdw'



in my input file for pw.x I get the warning:



 Message from routine set_vdw_corr:

 WARNING: unknown vdw correction (vdw_corr): mbd_vdw. No vdw correction 
used.



Is there something I'm missing for compiling libmbd with Quantum Espresso? I 
see 'make' does create a directory in qe-7.0 called MBD which seems to contain 
the source code for libmbd. Is there any other step I need to take? My linux OS 
is RHEL 7.9 for reference.

Thanks for any potential help,

John Stoppelman


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

Re: [QE-users] PWSCF v.7.0 unknown vdw correction (vdw_corr): mbd_vdw.

2022-05-09 Thread Hsin-Yu Ko 
Hi John,

Somehow the documentation is inconsistent with the source code. I did a quick 
search in `Modules/set_vdw_corr.f90` and found the following:
```
$ grep -n -C 3 MBD Modules/set_vdw_corr.f90
30-  CASE( 'TS', 'ts', 'ts-vdw', 'ts-vdW', 'tkatchenko-scheffler' )
31- ts_vdw = .TRUE.
32-
33:  CASE( 'MBD', 'mbd', 'many-body-dispersion' )
34- ts_vdw = .TRUE.
35- mbd_vdw = .TRUE.
36-
```

Please try vdw_corr = 'mbd' instead, and I will check if the documentation in 
the development version has been fixed.

Thank you,
Hsin-Yu

--
Hsin-Yu Ko
Postdoctoral Research Fellow
Department of Chemistry and Chemical Biology
Cornell University


From: users  on behalf of Stoppelman, 
John P 
Sent: Monday, May 9, 2022 7:38 AM
To: users@lists.quantum-espresso.org 
Subject: [QE-users] PWSCF v.7.0 unknown vdw correction (vdw_corr): mbd_vdw.


Hello,

I downloaded and compiled Quantum Espresso 7.0 from 
https://www.quantum-espresso.org/download-page/ and compiled using 
‘./configure’ and ‘make all’. When I include the option:



vdw_corr = 'mbd_vdw'



in my input file for pw.x I get the warning:



 Message from routine set_vdw_corr:

 WARNING: unknown vdw correction (vdw_corr): mbd_vdw. No vdw correction 
used.



Is there something I’m missing for compiling libmbd with Quantum Espresso? I 
see ‘make’ does create a directory in qe-7.0 called MBD which seems to contain 
the source code for libmbd. Is there any other step I need to take? My linux OS 
is RHEL 7.9 for reference.

Thanks for any potential help,

John Stoppelman


___
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 list users@lists.quantum-espresso.org
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[QE-users] PWSCF v.7.0 unknown vdw correction (vdw_corr): mbd_vdw.

2022-05-09 Thread Stoppelman, John P 
Hello,
I downloaded and compiled Quantum Espresso 7.0 from 
https://www.quantum-espresso.org/download-page/ and compiled using 
'./configure' and 'make all'. When I include the option:

vdw_corr = 'mbd_vdw'

in my input file for pw.x I get the warning:

 Message from routine set_vdw_corr:
 WARNING: unknown vdw correction (vdw_corr): mbd_vdw. No vdw correction 
used.

Is there something I'm missing for compiling libmbd with Quantum Espresso? I 
see 'make' does create a directory in qe-7.0 called MBD which seems to contain 
the source code for libmbd. Is there any other step I need to take? My linux OS 
is RHEL 7.9 for reference.
Thanks for any potential help,
John Stoppelman

___
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 list users@lists.quantum-espresso.org
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Re: [QE-users] An enquiry about momentum transfer in TDDFPT

2022-05-09 Thread Elio Physics 
Dear Iurii,

Thank you very much for your quick response.

Regards


From: users  on behalf of Iurii 
TIMROV via users 
Sent: Monday, May 9, 2022 6:45 AM
To: Quantum Espresso users Forum 
Subject: Re: [QE-users] An enquiry about momentum transfer in TDDFPT


Dear Elie,


> How do we set the (q1,q2,q3) variables in the turbo_eels.x input to point to 
> that specific path in the Brillouin zone?
> I was thinking that we can set them equal to the coordinates of the k-points 
> along the Gamma -K path


Correct


In the documentation it is written:

Variables:  q1, q2, q3

Description:The values of the transferred momentum q = (q1, q2, q3) in 
Cartesian coordinates in units of 2pi/a, where "a" is the lattice parameter.

Greetings,

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 Elio 
Physics 
Sent: Sunday, May 8, 2022 12:49:39 AM
To: Quantum Espresso users Forum
Subject: [QE-users] An enquiry about momentum transfer in TDDFPT

Dear all,

I have a question regarding the momentum transfer q in a TDDFPT calculation.
Let us say I want to calculate how the plasmon peak frequency changes along the 
Gamma-K path in a hexagonal lattice.
How do we set the (q1,q2,q3) variables in the turbo_eels.x input to point to 
that specific path in the Brillouin zone?
I was thinking that we can set them equal to the coordinates of the k-points 
along the Gamma -K path;  this would be then equivalent to a momentum transfer 
between the Gamma point and a specific point along the G-K path. Does this make 
sense?

Thanks in advance

Elie A Moujaess
Adjunct professor
Federal university of Rondonia
Porto Velho
Brazil
___
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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Re: [QE-users] An enquiry about momentum transfer in TDDFPT

2022-05-09 Thread Iurii TIMROV via users 
Dear Elie,


> How do we set the (q1,q2,q3) variables in the turbo_eels.x input to point to 
> that specific path in the Brillouin zone?
> I was thinking that we can set them equal to the coordinates of the k-points 
> along the Gamma -K path


Correct


In the documentation it is written:

Variables:  q1, q2, q3

Description:The values of the transferred momentum q = (q1, q2, q3) in 
Cartesian coordinates in units of 2pi/a, where "a" is the lattice parameter.

Greetings,

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 Elio 
Physics 
Sent: Sunday, May 8, 2022 12:49:39 AM
To: Quantum Espresso users Forum
Subject: [QE-users] An enquiry about momentum transfer in TDDFPT

Dear all,

I have a question regarding the momentum transfer q in a TDDFPT calculation.
Let us say I want to calculate how the plasmon peak frequency changes along the 
Gamma-K path in a hexagonal lattice.
How do we set the (q1,q2,q3) variables in the turbo_eels.x input to point to 
that specific path in the Brillouin zone?
I was thinking that we can set them equal to the coordinates of the k-points 
along the Gamma -K path;  this would be then equivalent to a momentum transfer 
between the Gamma point and a specific point along the G-K path. Does this make 
sense?

Thanks in advance

Elie A Moujaess
Adjunct professor
Federal university of Rondonia
Porto Velho
Brazil
___
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 list users@lists.quantum-espresso.org
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