Re: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field
Great, I have now added this to the manual to help new users. Den ons. 24. nov. 2021 kl. 22.04 skrev Fanmiao Kong < fanmiao.k...@materials.ox.ac.uk>: > Dear Nick, > > > > Thanks for your kind reminder. I will avoid using rar format later. > > I followed Daniel’s advice and have successfully re-run my calculation. > The problem has been solved. > > > > Best wishes, > > > > Fanmiao > > > > Fanmiao Kong > > Department of Materials, Trinity College, University of Oxford > > Tel: +44 (0)7529931806 / +86 13162054601 > > 16 Parks Road, OX1 3PH, Oxford, UK > > > > *From:* siesta-l-requ...@uam.es *On Behalf Of *Nick > Papior > *Sent:* 23 November 2021 12:07 > *To:* siesta-l > *Subject:* Re: [SIESTA-L] Problems of Siesta Calculation with Large > Electric Field > > > > HI, Daniel gave an excellent solution. > > > > Could you report back whether that solved the problem? > > > > Also for future reference, rar compressed files are generally not > advised... zip/tar.gz/tar.* are generally better (more portable). > > > > Den fre. 19. nov. 2021 kl. 22.05 skrev Fanmiao Kong < > fanmiao.k...@materials.ox.ac.uk>: > > Hi Nick, > > > > Thanks a lot for your reply! > > > > I attached the fdf and psf files here. > > > > Best regards, > > > > Fanmiao > > > > Fanmiao Kong > > Department of Materials, Trinity College, University of Oxford > > Tel: +44 (0)7529931806 / +86 13162054601 > > 16 Parks Road, OX1 3PH, Oxford, UK > > > > *From:* siesta-l-requ...@uam.es *On Behalf Of *Nick > Papior > *Sent:* 17 November 2021 21:08 > *To:* siesta-l > *Subject:* Re: [SIESTA-L] Problems of Siesta Calculation with Large > Electric Field > > > > Hi, > > > > Could you attach a complete workable example (fdf and psf files)? > > > > Den ons. 17. nov. 2021 kl. 22.03 skrev Fanmiao Kong < > fanmiao.k...@materials.ox.ac.uk>: > > Hi All, > > > > I met some bugs when I do Siesta calculation under electric field. > Sometimes the calculation doesn’t converge after 500 steps in a SCF cycle, > or sometimes the hydrogen atoms in my structure are ionized. I attached the > output file here where the calculation didn’t converge and I stopped it. I > suppose this is because of the very large electric field ( between 1.5 – > 2.1 V/Ang), since I don’t have this problem with electric field below 0.1 > V/Ang. Does anyone know how to fix this problem? > > > > Many thanks! > > > > Cheers, > > > > Fanmiao > > > > Fanmiao Kong > > Department of Materials, Trinity College, University of Oxford > > Tel: +44 (0)7529931806 / +86 13162054601 > > 16 Parks Road, OX1 3PH, Oxford, UK > > > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > > > > -- > > Kind regards Nick > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > > > > -- > > Kind regards Nick > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- Kind regards Nick -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
RE: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field
Dear Nick, Thanks for your kind reminder. I will avoid using rar format later. I followed Daniel’s advice and have successfully re-run my calculation. The problem has been solved. Best wishes, Fanmiao Fanmiao Kong Department of Materials, Trinity College, University of Oxford Tel: +44 (0)7529931806 / +86 13162054601 16 Parks Road, OX1 3PH, Oxford, UK From: siesta-l-requ...@uam.es On Behalf Of Nick Papior Sent: 23 November 2021 12:07 To: siesta-l Subject: Re: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field HI, Daniel gave an excellent solution. Could you report back whether that solved the problem? Also for future reference, rar compressed files are generally not advised... zip/tar.gz/tar.* are generally better (more portable). Den fre. 19. nov. 2021 kl. 22.05 skrev Fanmiao Kong mailto:fanmiao.k...@materials.ox.ac.uk>>: Hi Nick, Thanks a lot for your reply! I attached the fdf and psf files here. Best regards, Fanmiao Fanmiao Kong Department of Materials, Trinity College, University of Oxford Tel: +44 (0)7529931806 / +86 13162054601 16 Parks Road, OX1 3PH, Oxford, UK From: siesta-l-requ...@uam.es<mailto:siesta-l-requ...@uam.es> mailto:siesta-l-requ...@uam.es>> On Behalf Of Nick Papior Sent: 17 November 2021 21:08 To: siesta-l mailto:siesta-l@uam.es>> Subject: Re: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field Hi, Could you attach a complete workable example (fdf and psf files)? Den ons. 17. nov. 2021 kl. 22.03 skrev Fanmiao Kong mailto:fanmiao.k...@materials.ox.ac.uk>>: Hi All, I met some bugs when I do Siesta calculation under electric field. Sometimes the calculation doesn’t converge after 500 steps in a SCF cycle, or sometimes the hydrogen atoms in my structure are ionized. I attached the output file here where the calculation didn’t converge and I stopped it. I suppose this is because of the very large electric field ( between 1.5 – 2.1 V/Ang), since I don’t have this problem with electric field below 0.1 V/Ang. Does anyone know how to fix this problem? Many thanks! Cheers, Fanmiao Fanmiao Kong Department of Materials, Trinity College, University of Oxford Tel: +44 (0)7529931806 / +86 13162054601 16 Parks Road, OX1 3PH, Oxford, UK -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) -- Kind regards Nick -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) -- Kind regards Nick -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
RE: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field
Dear Danny, Thank you so much for the reply! It helped me a lot. I followed your suggestions and my calculation is running properly now! Best, Fanmiao Fanmiao Kong Department of Materials, Trinity College, University of Oxford Tel: +44 (0)7529931806 / +86 13162054601 16 Parks Road, OX1 3PH, Oxford, UK From: siesta-l-requ...@uam.es On Behalf Of Daniel Bennett Sent: 18 November 2021 21:30 To: siesta-l@uam.es Subject: Re: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field Dear Fanmiao, I have done a few calculations with fairly strong fields. I don't think it is a bug, but rather it is just very difficult to converge the SCF loop when the field is very strong. Two things that helped me were: * First, make sure that the SCF loop converges well at zero field. You'll need to test the different options like mixing weight and mixer history. Take a look in the manual, and this mailing list, since many people ask about this (myself included) * When doing calculations with an electric field, chaining several calculations together via the density matrix and gradually increasing the field greatly improves the convergence: instead of trying to do E= 2 V/Ang with no input *.DM, do a calculation at zero field, then take the *.DM and use it as an input for a calculation with e.g. E = 0.5 V/Ang, then use the *.DM from that for E = 1.0 V/Ang, and so on until you get to the desired field strength. The smaller the step size in field strength, the easier the convergence will be, but you will require more calculations, so it is up to you to decide Hope this helps, Danny Bennett From: siesta-l-requ...@uam.es<mailto:siesta-l-requ...@uam.es> mailto:siesta-l-requ...@uam.es>> on behalf of Nick Papior mailto:nickpap...@gmail.com>> Sent: 17 November 2021 22:07 To: siesta-l mailto:siesta-l@uam.es>> Subject: Re: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field Hi, Could you attach a complete workable example (fdf and psf files)? Den ons. 17. nov. 2021 kl. 22.03 skrev Fanmiao Kong mailto:fanmiao.k...@materials.ox.ac.uk>>: Hi All, I met some bugs when I do Siesta calculation under electric field. Sometimes the calculation doesn't converge after 500 steps in a SCF cycle, or sometimes the hydrogen atoms in my structure are ionized. I attached the output file here where the calculation didn't converge and I stopped it. I suppose this is because of the very large electric field ( between 1.5 - 2.1 V/Ang), since I don't have this problem with electric field below 0.1 V/Ang. Does anyone know how to fix this problem? Many thanks! Cheers, Fanmiao Fanmiao Kong Department of Materials, Trinity College, University of Oxford Tel: +44 (0)7529931806 / +86 13162054601 16 Parks Road, OX1 3PH, Oxford, UK -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) -- Kind regards Nick -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
Re: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field
HI, Daniel gave an excellent solution. Could you report back whether that solved the problem? Also for future reference, rar compressed files are generally not advised... zip/tar.gz/tar.* are generally better (more portable). Den fre. 19. nov. 2021 kl. 22.05 skrev Fanmiao Kong < fanmiao.k...@materials.ox.ac.uk>: > Hi Nick, > > > > Thanks a lot for your reply! > > > > I attached the fdf and psf files here. > > > > Best regards, > > > > Fanmiao > > > > Fanmiao Kong > > Department of Materials, Trinity College, University of Oxford > > Tel: +44 (0)7529931806 / +86 13162054601 > > 16 Parks Road, OX1 3PH, Oxford, UK > > > > *From:* siesta-l-requ...@uam.es *On Behalf Of *Nick > Papior > *Sent:* 17 November 2021 21:08 > *To:* siesta-l > *Subject:* Re: [SIESTA-L] Problems of Siesta Calculation with Large > Electric Field > > > > Hi, > > > > Could you attach a complete workable example (fdf and psf files)? > > > > Den ons. 17. nov. 2021 kl. 22.03 skrev Fanmiao Kong < > fanmiao.k...@materials.ox.ac.uk>: > > Hi All, > > > > I met some bugs when I do Siesta calculation under electric field. > Sometimes the calculation doesn’t converge after 500 steps in a SCF cycle, > or sometimes the hydrogen atoms in my structure are ionized. I attached the > output file here where the calculation didn’t converge and I stopped it. I > suppose this is because of the very large electric field ( between 1.5 – > 2.1 V/Ang), since I don’t have this problem with electric field below 0.1 > V/Ang. Does anyone know how to fix this problem? > > > > Many thanks! > > > > Cheers, > > > > Fanmiao > > > > Fanmiao Kong > > Department of Materials, Trinity College, University of Oxford > > Tel: +44 (0)7529931806 / +86 13162054601 > > 16 Parks Road, OX1 3PH, Oxford, UK > > > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > > > > -- > > Kind regards Nick > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- Kind regards Nick -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
RE: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field
Hi Nick, Thanks a lot for your reply! I attached the fdf and psf files here. Best regards, Fanmiao Fanmiao Kong Department of Materials, Trinity College, University of Oxford Tel: +44 (0)7529931806 / +86 13162054601 16 Parks Road, OX1 3PH, Oxford, UK From: siesta-l-requ...@uam.es On Behalf Of Nick Papior Sent: 17 November 2021 21:08 To: siesta-l Subject: Re: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field Hi, Could you attach a complete workable example (fdf and psf files)? Den ons. 17. nov. 2021 kl. 22.03 skrev Fanmiao Kong mailto:fanmiao.k...@materials.ox.ac.uk>>: Hi All, I met some bugs when I do Siesta calculation under electric field. Sometimes the calculation doesn’t converge after 500 steps in a SCF cycle, or sometimes the hydrogen atoms in my structure are ionized. I attached the output file here where the calculation didn’t converge and I stopped it. I suppose this is because of the very large electric field ( between 1.5 – 2.1 V/Ang), since I don’t have this problem with electric field below 0.1 V/Ang. Does anyone know how to fix this problem? Many thanks! Cheers, Fanmiao Fanmiao Kong Department of Materials, Trinity College, University of Oxford Tel: +44 (0)7529931806 / +86 13162054601 16 Parks Road, OX1 3PH, Oxford, UK -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) -- Kind regards Nick files.rar Description: files.rar -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
Re: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field
Dear Fanmiao, I have done a few calculations with fairly strong fields. I don't think it is a bug, but rather it is just very difficult to converge the SCF loop when the field is very strong. Two things that helped me were: * First, make sure that the SCF loop converges well at zero field. You'll need to test the different options like mixing weight and mixer history. Take a look in the manual, and this mailing list, since many people ask about this (myself included) * When doing calculations with an electric field, chaining several calculations together via the density matrix and gradually increasing the field greatly improves the convergence: instead of trying to do E= 2 V/Ang with no input *.DM, do a calculation at zero field, then take the *.DM and use it as an input for a calculation with e.g. E = 0.5 V/Ang, then use the *.DM from that for E = 1.0 V/Ang, and so on until you get to the desired field strength. The smaller the step size in field strength, the easier the convergence will be, but you will require more calculations, so it is up to you to decide Hope this helps, Danny Bennett From: siesta-l-requ...@uam.es on behalf of Nick Papior Sent: 17 November 2021 22:07 To: siesta-l Subject: Re: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field Hi, Could you attach a complete workable example (fdf and psf files)? Den ons. 17. nov. 2021 kl. 22.03 skrev Fanmiao Kong mailto:fanmiao.k...@materials.ox.ac.uk>>: Hi All, I met some bugs when I do Siesta calculation under electric field. Sometimes the calculation doesn’t converge after 500 steps in a SCF cycle, or sometimes the hydrogen atoms in my structure are ionized. I attached the output file here where the calculation didn’t converge and I stopped it. I suppose this is because of the very large electric field ( between 1.5 – 2.1 V/Ang), since I don’t have this problem with electric field below 0.1 V/Ang. Does anyone know how to fix this problem? Many thanks! Cheers, Fanmiao Fanmiao Kong Department of Materials, Trinity College, University of Oxford Tel: +44 (0)7529931806 / +86 13162054601 16 Parks Road, OX1 3PH, Oxford, UK -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) -- Kind regards Nick -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
Re: [SIESTA-L] Problems of Siesta Calculation with Large Electric Field
Hi, Could you attach a complete workable example (fdf and psf files)? Den ons. 17. nov. 2021 kl. 22.03 skrev Fanmiao Kong < fanmiao.k...@materials.ox.ac.uk>: > Hi All, > > > > I met some bugs when I do Siesta calculation under electric field. > Sometimes the calculation doesn’t converge after 500 steps in a SCF cycle, > or sometimes the hydrogen atoms in my structure are ionized. I attached the > output file here where the calculation didn’t converge and I stopped it. I > suppose this is because of the very large electric field ( between 1.5 – > 2.1 V/Ang), since I don’t have this problem with electric field below 0.1 > V/Ang. Does anyone know how to fix this problem? > > > > Many thanks! > > > > Cheers, > > > > Fanmiao > > > > Fanmiao Kong > > Department of Materials, Trinity College, University of Oxford > > Tel: +44 (0)7529931806 / +86 13162054601 > > 16 Parks Road, OX1 3PH, Oxford, UK > > > > -- > SIESTA is supported by the Spanish Research Agency (AEI) and by the > European H2020 MaX Centre of Excellence (http://www.max-centre.eu/) > -- Kind regards Nick -- SIESTA is supported by the Spanish Research Agency (AEI) and by the European H2020 MaX Centre of Excellence (http://www.max-centre.eu/)
