[QE-users] users Digest, Vol 204, Issue 12
Suraj P
surajp at iitkgp.ac.in
Mon Jul 15 15:26:01 CEST 2024
Thank you Lorenzo and Paolo for troubleshooting the input file error. Now the code is running smoothly.
Suraj
Research student, IIT Kharagpur
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Today's Topics:
1. Re: dipole correction with assume isolated ESM (Minoru Otani)
2. MPI error (Suraj P)
3. Re: MPI error (Paolo Giannozzi)
4. Re: MPI error (Lorenzo Paulatto)
5. Re: MPI error (Lorenzo Paulatto)
6. Re: dipole correction with assume isolated ESM (Lucian D. Filip)
----------------------------------------------------------------------
Message: 1
Date: Mon, 15 Jul 2024 10:59:05 +0900
From: Minoru Otani <otani at ccs.tsukuba.ac.jp>
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] dipole correction with assume isolated ESM
Message-ID: <4C175FD1-0CD7-485C-8ACC-B28DA0CA5762 at ccs.tsukuba.ac.jp>
Content-Type: text/plain; charset=us-ascii
Dear Lucian,
By using esm_bc=bc1, you can obtain the desired results. In this case, dipole correction is not necessary.
If you are calculating a system with no net dipole, the electrostatic potential on both sides will be flat and at the same level. On the other hand, if the system has a net dipole, the electrostatic potential on both sides will be flat, but the height of these flat regions will differ. This difference in height is related to the total dipole moment of the system.
The former can be correctly calculated even with conventional periodic boundary conditions, while the latter can be naturally calculated using ESM (esm_bc=bc1).
Best regards,
Minoru
-------------------------------------------------------------------------------------------------------
Minoru Otani, Ph.D., Professor
Center for Computational Sciences and Faculty of Pure and Applied Sciences,
University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
E-mail: otani at ccs.tsukuba.ac.jp
Web: https://www2.ccs.tsukuba.ac.jp/public/otani/
--------------------------------------------------------------------------------------------------------
> On Jul 12, 2024, at 18:47, Lucian D. Filip <lucian.filip at infim.ro> wrote:
>
> Hello all,
>
> Is it possible to use the " assume_isolated='esm' ", with the " esm_bc='bc2' " flag for a slab geometry and perform the dipole correction? I have tried with 'esm_field=0' but it doesn't seem to enforce the 0 field in vacuum. Rather it just performs a regular scf calculation with no applied field.
>
> I know about the '2D' option but that adds other complications because if I increase the slab thickness, the vacuum region becomes really big in order to ensure that the Coulombian cutoff is not too close to the slab to influence the slab.
>
> Is there a way to enforce a zero field in the vacuum region with ESM?
>
>
> Regards,
>
>
> Lucian
>
> --
> Dr. Lucian Dragos Filip
> National Institute of Materials Physics
> Atomistilor str. 405A, PO Box MG. 7
> Magurele, 077125
> Bucharest, Romania
> E-mail: lucian.filip at infim.ro
> Website: https://lucianfilip.wordpress.com/
>
> _______________________________________________
> 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 at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
------------------------------
Message: 2
Date: Mon, 15 Jul 2024 11:35:05 +0530 (IST)
From: Suraj P <surajp at iitkgp.ac.in>
To: users at lists.quantum-espresso.org
Subject: [QE-users] MPI error
Message-ID:
<658935827.2695548.1721023505157.JavaMail.zimbra at iitkgp.ac.in>
Content-Type: text/plain; charset="utf-8"
Dear QE users,
Im trying to do a relaxation calculation of a Copper unit cell doped with Nickel. 75 % of the atoms are doped with Nickel and the remaining atoms are Copper.
During the vc-relax calculation, Im getting an error message as follows, and the calculation gets automatically terminated:
______________________________________________________________________________________________
forrtl: severe (24): end-of-file during read, unit -5, file Internal List-Directed Read
Image PC Routine Line Source
pw.x 0000000000FE39AB Unknown Unknown Unknown
pw.x 00000000010143B2 Unknown Unknown Unknown
pw.x 0000000001013138 Unknown Unknown Unknown
pw.x 0000000000A03FCC read_cards_module 135 read_cards.f90
pw.x 00000000009230B6 read_input_mp_rea 67 read_input.f90
pw.x 000000000040BF62 MAIN__ 84 pwscf.f90
pw.x 000000000040BDD2 Unknown Unknown Unknown
libc-2.17.so 00007F893BB0A555 __libc_start_main Unknown Unknown
pw.x 000000000040BCE9 Unknown Unknown Unknown
______________________________________________________________________________
I have attached the input and output files herewith. Kindly help me in troubleshooting this issue.
Im using quantum_espresso-6.8 and openmpi-5.0.3 compiler.
Thanks regards
Suraj
Research student,IIT kharagpur
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Message: 3
Date: Mon, 15 Jul 2024 08:38:51 +0200
From: Paolo Giannozzi <paolo.giannozzi at uniud.it>
To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>,
Suraj P <surajp at iitkgp.ac.in>
Subject: Re: [QE-users] MPI error
Message-ID: <ba603840-b5ac-4f98-8962-67740ef8d393 at uniud.it>
Content-Type: text/plain; charset=UTF-8; format=flowed
Dear Suraj, it's not a "MPI error": it is an error reading the input
data, notably one of the "cards". There is nothing obviously wrong in
your data, but consider that errors can be produced by bad characters,
DOS CR-LF characters, missing EOL (end-of-line) in the last line, ...
PAolo
On 15/07/2024 08:05, Suraj P wrote:
>
> Dear QE users,
>
> Im trying to do a relaxation calculation of a Copper unit cell doped with Nickel. 75 % of the atoms are doped with Nickel and the remaining atoms are Copper.
> During the vc-relax calculation, Im getting an error message as follows, and the calculation gets automatically terminated:
> ______________________________________________________________________________________________
>
> forrtl: severe (24): end-of-file during read, unit -5, file Internal List-Directed Read
> Image PC Routine Line Source
> pw.x 0000000000FE39AB Unknown Unknown Unknown
> pw.x 00000000010143B2 Unknown Unknown Unknown
> pw.x 0000000001013138 Unknown Unknown Unknown
> pw.x 0000000000A03FCC read_cards_module 135 read_cards.f90
> pw.x 00000000009230B6 read_input_mp_rea 67 read_input.f90
> pw.x 000000000040BF62 MAIN__ 84 pwscf.f90
> pw.x 000000000040BDD2 Unknown Unknown Unknown
> libc-2.17.so 00007F893BB0A555 __libc_start_main Unknown Unknown
> pw.x 000000000040BCE9 Unknown Unknown Unknown
> ______________________________________________________________________________
>
>
> I have attached the input and output files herewith. Kindly help me in troubleshooting this issue.
> Im using quantum_espresso-6.8 and openmpi-5.0.3 compiler.
>
> Thanks regards
> Suraj
> Research student,IIT kharagpur
>
>
> _______________________________________________
> 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 at 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 206, 33100 Udine Italy, +39-0432-558216
X SCUOLA ENERGIE RINNOVABILI 16-21/9/2024 - PRE-ISCRIZIONE
https://agenda.infn.it/event/39573/
------------------------------
Message: 4
Date: Mon, 15 Jul 2024 09:49:16 +0200
From: Lorenzo Paulatto <lorenzo.paulatto at cnrs.fr>
To: <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] MPI error
Message-ID: <f10fea8f-fad5-4dca-8979-e621bc414d03 at cnrs.fr>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Hello,
if I understand correctly, you used the dash character ??? instead of
minus sign ?-? in many places all over the file.
On 15/07/2024 08:05, Suraj P wrote:
> Dear QE users,
>
> Im trying to do a relaxation calculation of a Copper unit cell doped with Nickel. 75 % of the atoms are doped with Nickel and the remaining atoms are Copper.
> During the vc-relax calculation, Im getting an error message as follows, and the calculation gets automatically terminated:
> ______________________________________________________________________________________________
>
> forrtl: severe (24): end-of-file during read, unit -5, file Internal List-Directed Read
> Image PC Routine Line Source
> pw.x 0000000000FE39AB Unknown Unknown Unknown
> pw.x 00000000010143B2 Unknown Unknown Unknown
> pw.x 0000000001013138 Unknown Unknown Unknown
> pw.x 0000000000A03FCC read_cards_module 135 read_cards.f90
> pw.x 00000000009230B6 read_input_mp_rea 67 read_input.f90
> pw.x 000000000040BF62 MAIN__ 84 pwscf.f90
> pw.x 000000000040BDD2 Unknown Unknown Unknown
> libc-2.17.so 00007F893BB0A555 __libc_start_main Unknown Unknown
> pw.x 000000000040BCE9 Unknown Unknown Unknown
> ______________________________________________________________________________
>
>
> I have attached the input and output files herewith. Kindly help me in troubleshooting this issue.
> Im using quantum_espresso-6.8 and openmpi-5.0.3 compiler.
>
> Thanks regards
> Suraj
> Research student,IIT kharagpur
>
> _______________________________________________
> 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 listusers at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Universit?
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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------------------------------
Message: 5
Date: Mon, 15 Jul 2024 09:53:38 +0200
From: Lorenzo Paulatto <lorenzo.paulatto at cnrs.fr>
To: <users at lists.quantum-espresso.org>
Subject: Re: [QE-users] MPI error
Message-ID: <7eff1ec7-d390-4ed4-b0f0-79766b2630c4 at cnrs.fr>
Content-Type: text/plain; charset="utf-8"; Format="flowed"
Nevermind, my monitor was playing tricks on me.
The actual problem is the line just before "ATOMIC_POSITIONS" which is
not empty, but contains several TAB characters. Remove it and the input
will work
hth
On 15/07/2024 09:49, Lorenzo Paulatto wrote:
>
> Hello,
>
> if I understand correctly, you used the dash character ??? instead of
> minus sign ?-? in many places all over the file.
>
> On 15/07/2024 08:05, Suraj P wrote:
>> Dear QE users,
>>
>> Im trying to do a relaxation calculation of a Copper unit cell doped with Nickel. 75 % of the atoms are doped with Nickel and the remaining atoms are Copper.
>> During the vc-relax calculation, Im getting an error message as follows, and the calculation gets automatically terminated:
>> ______________________________________________________________________________________________
>>
>> forrtl: severe (24): end-of-file during read, unit -5, file Internal List-Directed Read
>> Image PC Routine Line Source
>> pw.x 0000000000FE39AB Unknown Unknown Unknown
>> pw.x 00000000010143B2 Unknown Unknown Unknown
>> pw.x 0000000001013138 Unknown Unknown Unknown
>> pw.x 0000000000A03FCC read_cards_module 135 read_cards.f90
>> pw.x 00000000009230B6 read_input_mp_rea 67 read_input.f90
>> pw.x 000000000040BF62 MAIN__ 84 pwscf.f90
>> pw.x 000000000040BDD2 Unknown Unknown Unknown
>> libc-2.17.so 00007F893BB0A555 __libc_start_main Unknown Unknown
>> pw.x 000000000040BCE9 Unknown Unknown Unknown
>> ______________________________________________________________________________
>>
>>
>> I have attached the input and output files herewith. Kindly help me in troubleshooting this issue.
>> Im using quantum_espresso-6.8 and openmpi-5.0.3 compiler.
>>
>> Thanks regards
>> Suraj
>> Research student,IIT kharagpur
>>
>> _______________________________________________
>> 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 listusers at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
> --
> Dr. Lorenzo Paulatto
> IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Universit?
> 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
--
Dr. Lorenzo Paulatto
IdR @ IMPMC - CNRS UMR 7590 & Sorbonne Universit?
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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------------------------------
Message: 6
Date: Mon, 15 Jul 2024 12:09:47 +0300
From: "Lucian D. Filip" <lucian.filip at infim.ro>
To: users at lists.quantum-espresso.org
Subject: Re: [QE-users] dipole correction with assume isolated ESM
Message-ID: <61fe331f-678f-4c97-81a0-d83a1a4d1d32 at infim.ro>
Content-Type: text/plain; charset=UTF-8; format=flowed
Dear Minoru,
Thank you very much for this clarification! I finally understand it now!
I have now tested my example and saw that there is no difference between
a 10 angstrom vacuum region and a 20 vacuum region on either side of my
slab. This is good news for me for my future calculations!
Best regards,
Lucian
On 15-Jul-24 4:59 AM, Minoru Otani wrote:
> Dear Lucian,
>
> By using esm_bc=bc1, you can obtain the desired results. In this case, dipole correction is not necessary.
>
> If you are calculating a system with no net dipole, the electrostatic potential on both sides will be flat and at the same level. On the other hand, if the system has a net dipole, the electrostatic potential on both sides will be flat, but the height of these flat regions will differ. This difference in height is related to the total dipole moment of the system.
>
> The former can be correctly calculated even with conventional periodic boundary conditions, while the latter can be naturally calculated using ESM (esm_bc=bc1).
>
> Best regards,
> Minoru
> -------------------------------------------------------------------------------------------------------
> Minoru Otani, Ph.D., Professor
> Center for Computational Sciences and Faculty of Pure and Applied Sciences,
> University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
> E-mail: otani at ccs.tsukuba.ac.jp
> Web: https://www2.ccs.tsukuba.ac.jp/public/otani/
> --------------------------------------------------------------------------------------------------------
>
>> On Jul 12, 2024, at 18:47, Lucian D. Filip <lucian.filip at infim.ro> wrote:
>>
>> Hello all,
>>
>> Is it possible to use the " assume_isolated='esm' ", with the " esm_bc='bc2' " flag for a slab geometry and perform the dipole correction? I have tried with 'esm_field=0' but it doesn't seem to enforce the 0 field in vacuum. Rather it just performs a regular scf calculation with no applied field.
>>
>> I know about the '2D' option but that adds other complications because if I increase the slab thickness, the vacuum region becomes really big in order to ensure that the Coulombian cutoff is not too close to the slab to influence the slab.
>>
>> Is there a way to enforce a zero field in the vacuum region with ESM?
>>
>>
>> Regards,
>>
>>
>> Lucian
>>
>> --
>> Dr. Lucian Dragos Filip
>> National Institute of Materials Physics
>> Atomistilor str. 405A, PO Box MG. 7
>> Magurele, 077125
>> Bucharest, Romania
>> E-mail: lucian.filip at infim.ro
>> Website: https://lucianfilip.wordpress.com/
>>
>> _______________________________________________
>> 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 at lists.quantum-espresso.org
>> https://lists.quantum-espresso.org/mailman/listinfo/users
> _______________________________________________
> 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 at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
--
Dr. Lucian Dragos Filip
National Institute of Materials Physics
Atomistilor str. 405A, PO Box MG. 7
Magurele, 077125
Bucharest, Romania
E-mail: lucian.filip at infim.ro
Website: https://lucianfilip.wordpress.com/
------------------------------
Subject: Digest Footer
_______________________________________________
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 at lists.quantum-espresso.org
https://lists.quantum-espresso.org/mailman/listinfo/users
------------------------------
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