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 > Send users mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.quantum-espresso.org/mailman/listinfo/users > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of users digest..." > > > 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 <[email protected]> > To: Quantum ESPRESSO users Forum <[email protected]> > Subject: Re: [QE-users] vc-relax with PBE0 not converging > Message-ID: > <CABx8G42_qbJQUF8ZUqOxUH_RBcbKUbSaM0fz_H6FrtZ9bTy=f...@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/[email protected]/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 <[email protected]> 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 [email protected] >> https://lists.quantum-espresso.org/mailman/listinfo/users > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.quantum-espresso.org/pipermail/users/attachments/20210130/409192bb/attachment-0001.html> > -------------- next part -------------- > A non-text attachment was scrubbed... > Name: image.png > Type: image/png > Size: 28643 bytes > Desc: not available > URL: > <http://lists.quantum-espresso.org/pipermail/users/attachments/20210130/409192bb/attachment-0001.png> > > ------------------------------ > > Message: 2 > Date: Sun, 31 Jan 2021 04:26:37 +0000 > From: valeria arteaga mu?iz <[email protected]> > To: "[email protected] " > <[email protected]> > Subject: [QE-users] crystal definition > Message-ID: > > <ph0pr14mb43597bc28fc16ee61837b0dec9...@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 > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.quantum-espresso.org/pipermail/users/attachments/20210131/62cc5239/attachment-0001.html> > > ------------------------------ > > Message: 3 > Date: Sun, 31 Jan 2021 06:39:09 +0000 > From: Husak Michal <[email protected]> > To: Quantum ESPRESSO users Forum <[email protected]> > Subject: Re: [QE-users] crystal definition > Message-ID: <[email protected]> > 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 <[email protected]> on behalf of > valeria arteaga mu?iz <[email protected]> > Sent: Sunday, January 31, 2021 5:26:37 AM > To: [email protected] > 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 <[email protected]> > To: Quantum ESPRESSO users Forum <[email protected]> > Subject: Re: [QE-users] crystal definition > Message-ID: > > <ph0pr14mb43592d1b9336fcea716e1a25c9...@ph0pr14mb4359.namprd14.prod.outlook.com> > > Content-Type: text/plain; charset="windows-1252" > > Could you please be more specific on this? > > From: Husak Michal<mailto:[email protected]> > Sent: Saturday, January 30, 2021 11:39 PM > To: Quantum ESPRESSO users Forum<mailto:[email protected]> > 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 <[email protected]> on behalf of > valeria arteaga mu?iz <[email protected]> > Sent: Sunday, January 31, 2021 5:26:37 AM > To: [email protected] > 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 [email protected] > https://lists.quantum-espresso.org/mailman/listinfo/users > > -------------- next part -------------- > An HTML attachment was scrubbed... > URL: > <http://lists.quantum-espresso.org/pipermail/users/attachments/20210131/777a8bba/attachment-0001.html> > > ------------------------------ > > Message: 5 > Date: Sun, 31 Jan 2021 09:17:35 +0100 > From: Stefano Baroni <[email protected]> > To: Quantum ESPRESSO users Forum <[email protected]> > Subject: Re: [QE-users] crystal definition > Message-ID: <[email protected]> > 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 <[email protected]> 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 <[email protected]> on behalf of >> valeria arteaga mu?iz <[email protected]> >> Sent: Sunday, January 31, 2021 5:26:37 AM >> To: [email protected] >> 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 [email protected] >> https://lists.quantum-espresso.org/mailman/listinfo/users > > > > ------------------------------ > > Message: 6 > Date: Sun, 31 Jan 2021 09:18:51 +0100 > From: Tone Kokalj <[email protected]> > To: [email protected] > Subject: Re: [QE-users] crystal definition > Message-ID: <[email protected]> > 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 <[email protected]> > To: Quantum ESPRESSO users Forum <[email protected]> > Subject: Re: [QE-users] crystal definition > Message-ID: <[email protected]> > 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 > [email protected] > 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/ * * * D I S C L A I M E R * * * This e-mail may contain privileged information and is intended solely for the individual named. If you are not the named addressee you should not disseminate, distribute or copy this e-mail. Please notify the sender immediately by e-mail if you have received this e-mail in error and destroy it from your system. 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