[QE-users] users Digest, Vol 162, Issue 30
Mayuri Bora
mayu219 at tezu.ernet.in
Sun Jan 31 16:47:00 CET 2021
Hello Everyone,
>From more than a month i am trying to simulate a 2D heterostructure system
including SOC and starting magnetization using PBE-GGA and DFT-D. But
repeatedly i am getting a segmentation fault in it? I will be grateful if
i get some help and suggestion in this regard.
The segmentation error looks as shown below-
cp: missing destination file operand after
‘/global/home/sushantk/mayuri/QAHE/’
Try 'cp --help' for more information.
forrtl: severe (174): SIGSEGV, segmentation fault occurred
Image PC Routine Line Source
libintlc.so.5 00007FAFB859FC05 Unknown Unknown Unknown
libintlc.so.5 00007FAFB859D827 Unknown Unknown Unknown
libifcoremt.so.5 00007FAFBA32C962 Unknown Unknown Unknown
libifcoremt.so.5 00007FAFBA32C7B6 Unknown Unknown Unknown
libifcoremt.so.5 00007FAFBA281CAD Unknown Unknown Unknown
libifcoremt.so.5 00007FAFBA293FAD Unknown Unknown Unknown
libpthread.so.0 00007FAFBA816100 Unknown Unknown Unknown
pw.x 000000000053E3E3 Unknown Unknown Unknown
pw.x 00000000005354DD Unknown Unknown Unknown
pw.x 0000000000529284 Unknown Unknown Unknown
pw.x 0000000000524E11 Unknown Unknown Unknown
pw.x 000000000057C092 Unknown Unknown Unknown
pw.x 00000000004DB3B9 Unknown Unknown Unknown
pw.x 0000000000406670 Unknown Unknown Unknown
pw.x 0000000000406523 Unknown Unknown Unknown
pw.x 000000000040648E Unknown Unknown Unknown
libc.so.6 00007FAFB81E6B15 Unknown Unknown Unknown
pw.x 0000000000406399 Unknown Unknown Unknown
forrtl: error (69): process interrupted (SIGINT)
Image PC Routine Line Source
libintlc.so.5 00007F7E564B2C05 Unknown Unknown Unknown
libintlc.so.5 00007F7E564B0827 Unknown Unknown Unknown
libifcoremt.so.5 00007F7E5823F962 Unknown Unknown Unknown
libifcoremt.so.5 00007F7E5823F7B6 Unknown Unknown Unknown
libifcoremt.so.5 00007F7E58194CAD Unknown Unknown Unknown
libifcoremt.so.5 00007F7E581A77F7 Unknown Unknown Unknown
libpthread.so.0 00007F7E58729100 Unknown Unknown Unknown
libiomp5.so 00007F7E5674C005 Unknown Unknown Unknown
libiomp5.so 00007F7E56749810 Unknown Unknown Unknown
libiomp5.so 00007F7E567529AB Unknown Unknown Unknown
pw.x 000000000052EC12 Unknown Unknown Unknown
libiomp5.so 00007F7E567A9CB3 Unknown Unknown Unknown
libiomp5.so 00007F7E56778437 Unknown Unknown Unknown
libiomp5.so 00007F7E5677960B Unknown Unknown Unknown
libiomp5.so 00007F7E56752518 Unknown Unknown Unknown
pw.x 000000000052E187 Unknown Unknown Unknown
regards
Mayuri
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> Today's Topics:
>
> 1. Re: vc-relax with PBE0 not converging (Giovani Rech)
> 2. crystal definition (valeria arteaga mu?iz)
> 3. Re: crystal definition (Husak Michal)
> 4. Re: crystal definition (valeria arteaga mu?iz)
> 5. Re: crystal definition (Stefano Baroni)
> 6. Re: crystal definition (Tone Kokalj)
> 7. Re: crystal definition (Tone Kokalj)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 30 Jan 2021 15:28:52 -0300
> From: Giovani Rech <gio.pi.rech at gmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] vc-relax with PBE0 not converging
> Message-ID:
> <CABx8G42_qbJQUF8ZUqOxUH_RBcbKUbSaM0fz_H6FrtZ9bTy=FQ at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Dear Xavier,
> I've faced the same issue a while back while using scan-rvv10. The
> pressure
> would not converge with the pseudo-potential that I was using (ONCV). For
> my case (
> https://www.mail-archive.com/users@lists.quantum-espresso.org/msg36102.html)
> the issue was solved when I changed the PP to one that was built using
> SCAN.
> Please try to use one of the PP found here:
> https://yaoyi92.github.io/scan-tm-pseudopotentials.html or even look for a
> PP built using PBE0.
>
> Hope this helps,
>
> *Giovani Rech*
>
> Materials Physics and Advanced Ceramics
> Universidade de Caxias do Sul
> 95070-560 Caxias do Sul - RS, Brazil
> orcid.org/0000-0003-0476-2056
>
>
>
> On Mon, Jan 25, 2021 at 12:19 PM Bidault, Xavier <xavbdlt at uic.edu> wrote:
>
>> Hello,
>>
>> I have a molecular crystal (1 unit cell = 56 atoms). I use SG15 ONCV 1.2
>> pseudopotential and Grimme D2 correction.
>> Using vc-relax with PBE, the structure converges, no problem.
>> But with PBE0, density and pressure oscillate without dampening (see
>> figure below - Pressure remains negative, and not close to zero). Is
>> there
>> any particular strategy with PBE0?
>>
>> - vc-relax with PBE and then starting from the result and use PBE0?
>> - relax with PBE0 and then vc-relax?
>> - any simulation parameter to change (ion dynamics and/or cell
>> dynamics - currently BFGS)?
>> - any strategy with PBE0?
>>
>>
>> Thank you,
>> Xavier
>>
>> _______________________________________________
>> 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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> ------------------------------
>
> Message: 2
> Date: Sun, 31 Jan 2021 04:26:37 +0000
> From: valeria arteaga mu?iz <valitzelar at hotmail.com>
> To: "users at lists.quantum-espresso.org "
> <users at lists.quantum-espresso.org>
> Subject: [QE-users] crystal definition
> Message-ID:
> <PH0PR14MB43597BC28FC16EE61837B0DEC9B79 at PH0PR14MB4359.namprd14.prod.outlook.com>
>
> Content-Type: text/plain; charset="windows-1252"
>
> Hello everyone.
>
> I have been working for a couple of months with quantum espresso and still
> there are some things that get me confused. I hope you can help me.
> If we wanted to define a BCC crystal (lets say) we could make use of the
> ibrav=3 parameter. With this, we would have a bcc structure with one atom
> per cell (?). I don?t know how can that be possible if the bcc cell is
> supposed to have two atoms per cell (1/8 contribution of 8 corner atoms +
> 1 contribution of a middle atom). When I use xcrysden for visualization
> just setting ibrav =3, I get the complete bcc structure.
>
> I also have tried to create my bcc crystal from scratch using ibrav=0 and
> placing the atomic positions at the corner and other atom at 0.5 0.5 0.5
> (center), which leads to 2 atoms per unit cell. When I make scf
> calculations for this case I get around twice the total energy I get in
> previous case (using ibrav=3). I wonder what is the correct way to use
> this.
>
>
> Thanks for your clarifications,
> Valeria
>
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> ------------------------------
>
> Message: 3
> Date: Sun, 31 Jan 2021 06:39:09 +0000
> From: Husak Michal <Michal.Husak at vscht.cz>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] crystal definition
> Message-ID: <fc259b1b99d84844bedadf9938ac01e3 at vscht.cz>
> Content-Type: text/plain; charset="Windows-1252"
>
> Forget this method.
> Get a CIF file for the structure you want to stady and
> use the space group based crystal definition ...
> ________________________________
> From: users <users-bounces at lists.quantum-espresso.org> on behalf of
> valeria arteaga mu?iz <valitzelar at hotmail.com>
> Sent: Sunday, January 31, 2021 5:26:37 AM
> To: users at lists.quantum-espresso.org
> Subject: [QE-users] crystal definition
>
> Hello everyone.
>
> I have been working for a couple of months with quantum espresso and still
> there are some things that get me confused. I hope you can help me.
> If we wanted to define a BCC crystal (lets say) we could make use of the
> ibrav=3 parameter. With this, we would have a bcc structure with one atom
> per cell (?). I don?t know how can that be possible if the bcc cell is
> supposed to have two atoms per cell (1/8 contribution of 8 corner atoms +
> 1 contribution of a middle atom). When I use xcrysden for visualization
> just setting ibrav =3, I get the complete bcc structure.
>
> I also have tried to create my bcc crystal from scratch using ibrav=0 and
> placing the atomic positions at the corner and other atom at 0.5 0.5 0.5
> (center), which leads to 2 atoms per unit cell. When I make scf
> calculations for this case I get around twice the total energy I get in
> previous case (using ibrav=3). I wonder what is the correct way to use
> this.
>
>
> Thanks for your clarifications,
> Valeria
>
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 31 Jan 2021 06:56:35 +0000
> From: valeria arteaga mu?iz <valitzelar at hotmail.com>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] crystal definition
> Message-ID:
> <PH0PR14MB43592D1B9336FCEA716E1A25C9B79 at PH0PR14MB4359.namprd14.prod.outlook.com>
>
> Content-Type: text/plain; charset="windows-1252"
>
> Could you please be more specific on this?
>
> From: Husak Michal<mailto:Michal.Husak at vscht.cz>
> Sent: Saturday, January 30, 2021 11:39 PM
> To: Quantum ESPRESSO users Forum<mailto:users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] crystal definition
>
> Forget this method.
> Get a CIF file for the structure you want to stady and
> use the space group based crystal definition ...
> ________________________________
> From: users <users-bounces at lists.quantum-espresso.org> on behalf of
> valeria arteaga mu?iz <valitzelar at hotmail.com>
> Sent: Sunday, January 31, 2021 5:26:37 AM
> To: users at lists.quantum-espresso.org
> Subject: [QE-users] crystal definition
>
> Hello everyone.
>
> I have been working for a couple of months with quantum espresso and still
> there are some things that get me confused. I hope you can help me.
> If we wanted to define a BCC crystal (lets say) we could make use of the
> ibrav=3 parameter. With this, we would have a bcc structure with one atom
> per cell (?). I don?t know how can that be possible if the bcc cell is
> supposed to have two atoms per cell (1/8 contribution of 8 corner atoms +
> 1 contribution of a middle atom). When I use xcrysden for visualization
> just setting ibrav =3, I get the complete bcc structure.
>
> I also have tried to create my bcc crystal from scratch using ibrav=0 and
> placing the atomic positions at the corner and other atom at 0.5 0.5 0.5
> (center), which leads to 2 atoms per unit cell. When I make scf
> calculations for this case I get around twice the total energy I get in
> previous case (using ibrav=3). I wonder what is the correct way to use
> this.
>
>
> Thanks for your clarifications,
> Valeria
>
> _______________________________________________
> Quantum ESPRESSO is supported by MaX
> (www.max-centre.eu<http://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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>
> ------------------------------
>
> Message: 5
> Date: Sun, 31 Jan 2021 09:17:35 +0100
> From: Stefano Baroni <baroni at sissa.it>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] crystal definition
> Message-ID: <3EA3BD80-BD63-4B6C-AA2B-8F7889F0F7B8 at sissa.it>
> Content-Type: text/plain; charset=utf-8
>
> Valeria: your question is answered, e.g., at page 10 of the eighth
> edition of Kittel?s solid state textbook. I am afraid you?ll have to go
> through as many as 9 pages to arrive at the point, but they are full of
> figures. Hope this helps. SB
>
> ___
> Stefano Baroni, Trieste -- http://stefano.baroni.me
>
>> On 31 Jan 2021, at 07:39, Husak Michal <Michal.Husak at vscht.cz> wrote:
>>
>> ?Forget this method.
>> Get a CIF file for the structure you want to stady and
>> use the space group based crystal definition ...
>> ________________________________
>> From: users <users-bounces at lists.quantum-espresso.org> on behalf of
>> valeria arteaga mu?iz <valitzelar at hotmail.com>
>> Sent: Sunday, January 31, 2021 5:26:37 AM
>> To: users at lists.quantum-espresso.org
>> Subject: [QE-users] crystal definition
>>
>> Hello everyone.
>>
>> I have been working for a couple of months with quantum espresso and
>> still there are some things that get me confused. I hope you can help
>> me.
>> If we wanted to define a BCC crystal (lets say) we could make use of the
>> ibrav=3 parameter. With this, we would have a bcc structure with one
>> atom per cell (?). I don?t know how can that be possible if the bcc cell
>> is supposed to have two atoms per cell (1/8 contribution of 8 corner
>> atoms + 1 contribution of a middle atom). When I use xcrysden for
>> visualization just setting ibrav =3, I get the complete bcc structure.
>>
>> I also have tried to create my bcc crystal from scratch using ibrav=0
>> and placing the atomic positions at the corner and other atom at 0.5 0.5
>> 0.5 (center), which leads to 2 atoms per unit cell. When I make scf
>> calculations for this case I get around twice the total energy I get in
>> previous case (using ibrav=3). I wonder what is the correct way to use
>> this.
>>
>>
>> Thanks for your clarifications,
>> Valeria
>>
>> _______________________________________________
>> 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: 6
> Date: Sun, 31 Jan 2021 09:18:51 +0100
> From: Tone Kokalj <tone.kokalj at ijs.si>
> To: users at lists.quantum-espresso.org
> Subject: Re: [QE-users] crystal definition
> Message-ID: <6e91ca3fdfd5b1356f0c1211c3fc7f38ff7aee45.camel at ijs.si>
> Content-Type: text/plain; charset="UTF-8"
>
> On Sun, 2021-01-31 at 06:39 +0000, Husak Michal wrote:
>> Forget this method.
>> Get a CIF file for the structure you want to stady and
>> use the space group based crystal definition ...
>
> I completely disagree.
>
> What Valeria described is all correct. The question to answer is this:
> why is the total energy with ibrav=3 twice smaller than that for
> ibrav=0 with two atoms in the unit cell.
>
> With ibrav=3, there is one atom per primitive bcc unit cell, whereas
> with ibrav=0 the bcc crystal was described as primitive-cubic with two
> atoms per unit-cell. In xcrysden these are called primitive vs
> conventional cell mode. To understand the difference, load the ibrav=3
> input in xcrysden and switch between the two (i.e. Display-->Primitive
> Cell Mode vs. Display-->Conventional Cell Mode).
>
> Best regards, Tone
> --
> Jo?ef Stefan Institute, Ljubljana, Slovenia
>
>
>
>
> ------------------------------
>
> Message: 7
> Date: Sun, 31 Jan 2021 09:25:01 +0100
> From: Tone Kokalj <tone.kokalj at ijs.si>
> To: Quantum ESPRESSO users Forum <users at lists.quantum-espresso.org>
> Subject: Re: [QE-users] crystal definition
> Message-ID: <d67d60645a96aa950fd28a028332759385d73943.camel at ijs.si>
> Content-Type: text/plain; charset="UTF-8"
>
> On Sun, 2021-01-31 at 09:18 +0100, Tone Kokalj wrote:
>>
>> What Valeria described is all correct. The question to answer is
>> this: why is the total energy with ibrav=3 twice smaller ...
>
> Twice smaller in magnitude is what I actually meant. Tone
> --
> Jo?ef Stefan Institute, Ljubljana, Slovenia
>
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> users mailing list
> users at lists.quantum-espresso.org
> https://lists.quantum-espresso.org/mailman/listinfo/users
>
> ------------------------------
>
> End of users Digest, Vol 162, Issue 30
> **************************************
>
Mayuri Bora
INSPIRE Fellow
Advanced Functional Material Laboratory
Tezpur University
Napaam
http://www.tezu.ernet.in/afml/
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