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ksyang2013 / aimsgb

Ab-initio Interface Materials Simulation Project for Grain Boundaries (AIMSGB)
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pip installation of aimsgb not giving the same as your homepage #1

Closed AleksBL closed 1 year ago

AleksBL commented 3 years ago

Hi im trying to do some graphene grain boundary calculations, and your program seemed fit to do so, but I have encountered some strange behavior of your python code. When comparing the results from your webpage and the python package (installed with pip), the results with the same values of sigma, rotation axis, GB-plane do not agree. The lattices from the python code do not seem to be hexagonal anymore and overall seems twisted.

jic198 commented 3 years ago

Hi,

Thanks for letting us know the issue. Could you tell me the GB you are trying to build? Input structure, sigma, rotation axis, etc. I am trying to reproduce the inconsistency.

Thanks, Jianli

On Tue, Dec 15, 2020 at 12:26 AM AleksBL notifications@github.com wrote:

Hi im trying to do some graphene grain boundary calculations, and your program seemed fit to do so, but I have encountered some strange behavior of your python code. When comparing the results from your webpage and the python package (installed with pip), the results with the same values of sigma, rotation axis, GB-plane do not agree. The lattices from the python code do not seem to be hexagonal anymore and overall seems twisted.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/ksyang2013/aimsgb/issues/1__;!!Mih3wA!WmSeeQFm2lxI1PRM6DV1XZgY9ItQMPL-AUXn0LSLxO74WZ-skKJwqqpKxHZBdqHPJg$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AEM7HVEWXRC66MTY3GJ7JBDSU4MSRANCNFSM4U36TDPQ__;!!Mih3wA!WmSeeQFm2lxI1PRM6DV1XZgY9ItQMPL-AUXn0LSLxO74WZ-skKJwqqpKxHZGE2rZhw$ .

AleksBL commented 3 years ago

Hi,

Here is the python-script Im running together with two pictures of the two resulting outputs from the python module and your website. I have put sigma = 5, rotation axis=[001] and GB plane to [2 -1 0] in both cases. The code generates the initial .fdf file using something called "sisl" which can be installed with pip in python. If you want it try this, then just install sisl. The top of the python script is just functions for making fdf to xsf and such things, the setup happens from line 112.

Best regards,

Aleksander Bach Lorentzen, PhD student at DTU

Fra: Jianli Cheng notifications@github.com Sendt: 15. december 2020 23:43:46 Til: ksyang2013/aimsgb Cc: Aleksander Lorentzen; Author Emne: Re: [ksyang2013/aimsgb] pip installation of aimsgb not giving the same as your homepage (#1)

Hi,

Thanks for letting us know the issue. Could you tell me the GB you are trying to build? Input structure, sigma, rotation axis, etc. I am trying to reproduce the inconsistency.

Thanks, Jianli

On Tue, Dec 15, 2020 at 12:26 AM AleksBL notifications@github.com wrote:

Hi im trying to do some graphene grain boundary calculations, and your program seemed fit to do so, but I have encountered some strange behavior of your python code. When comparing the results from your webpage and the python package (installed with pip), the results with the same values of sigma, rotation axis, GB-plane do not agree. The lattices from the python code do not seem to be hexagonal anymore and overall seems twisted.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/ksyang2013/aimsgb/issues/1__;!!Mih3wA!WmSeeQFm2lxI1PRM6DV1XZgY9ItQMPL-AUXn0LSLxO74WZ-skKJwqqpKxHZBdqHPJg$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AEM7HVEWXRC66MTY3GJ7JBDSU4MSRANCNFSM4U36TDPQ__;!!Mih3wA!WmSeeQFm2lxI1PRM6DV1XZgY9ItQMPL-AUXn0LSLxO74WZ-skKJwqqpKxHZGE2rZhw$ .

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AleksBL commented 3 years ago

I of course forgot to put the file in the previous mail.

Fra: Aleksander Lorentzen Sendt: 16. december 2020 08:39:00 Til: ksyang2013/aimsgb; ksyang2013/aimsgb Cc: Author Emne: Sv: [ksyang2013/aimsgb] pip installation of aimsgb not giving the same as your homepage (#1)

Hi,

Here is the python-script Im running together with two pictures of the two resulting outputs from the python module and your website. I have put sigma = 5, rotation axis=[001] and GB plane to [2 -1 0] in both cases. The code generates the initial .fdf file using something called "sisl" which can be installed with pip in python. If you want it try this, then just install sisl. The top of the python script is just functions for making fdf to xsf and such things, the setup happens from line 112.

Best regards,

Aleksander Bach Lorentzen, PhD student at DTU

Fra: Jianli Cheng notifications@github.com Sendt: 15. december 2020 23:43:46 Til: ksyang2013/aimsgb Cc: Aleksander Lorentzen; Author Emne: Re: [ksyang2013/aimsgb] pip installation of aimsgb not giving the same as your homepage (#1)

Hi,

Thanks for letting us know the issue. Could you tell me the GB you are trying to build? Input structure, sigma, rotation axis, etc. I am trying to reproduce the inconsistency.

Thanks, Jianli

On Tue, Dec 15, 2020 at 12:26 AM AleksBL notifications@github.com wrote:

Hi im trying to do some graphene grain boundary calculations, and your program seemed fit to do so, but I have encountered some strange behavior of your python code. When comparing the results from your webpage and the python package (installed with pip), the results with the same values of sigma, rotation axis, GB-plane do not agree. The lattices from the python code do not seem to be hexagonal anymore and overall seems twisted.

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://urldefense.com/v3/__https://github.com/ksyang2013/aimsgb/issues/1__;!!Mih3wA!WmSeeQFm2lxI1PRM6DV1XZgY9ItQMPL-AUXn0LSLxO74WZ-skKJwqqpKxHZBdqHPJg$, or unsubscribe https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AEM7HVEWXRC66MTY3GJ7JBDSU4MSRANCNFSM4U36TDPQ__;!!Mih3wA!WmSeeQFm2lxI1PRM6DV1XZgY9ItQMPL-AUXn0LSLxO74WZ-skKJwqqpKxHZGE2rZhw$ .

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/ksyang2013/aimsgb/issues/1#issuecomment-745613864, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AR7C74XRAMDNT6K6SX33BJTSU7RCFANCNFSM4U36TDPQ.

AleksBL commented 3 years ago

Hi, I hope my previous emails reached you, but if they didnt here is the input files again

Best regards, Aleksander input_and_pythoncode.tar.gz

jic198 commented 3 years ago

Hi Aleksander,

I am so sorry for the delayed reply.

I looked at your structure, which is a 2D material. Unfortunately, aimsgb has an issue of creating a GB for an initial structure like that. The created GB is skewed. I have always hoped to fix this problem, but don't get the time to do that. I am sorry for the inconvenience.

Thanks, Jianli

jic198 commented 1 year ago

The recently updated code should be able to generate a graphene grain boundary structure. An example can be found here.