 Re: Phonon calculations ( No.1 ) |
- Date: 2022/12/05 08:54
- Name: Masanobu Miyata <m-miyata@jaist.ac.jp>
- Hi．
An interface for OpenMX is implemented in the phonon computation code ALAMODE. Therefore, phonon calculations can be performed by using ALAMODE and OpenMX.
Please refer to the ALAMODE tutorial for details. https://alamode.readthedocs.io/en/latest/tutorial.html
Best regards,
Miyata
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| Re: Phonon calculations ( No.2 ) |
- Date: 2022/12/05 12:40
- Name: Mehdi Vejdanihemmat <m.vejdanih@gmail.com>
- Dear Dr. Miyata,
Thank you very much. It was very helpful.
Best wishes,
Mehdi Vejdanihemmat
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| Re: Phonon calculations ( No.3 ) |
- Date: 2022/12/05 15:16
- Name: T. Ozaki
- Hi,
With the combination of OpenMX and ALAMODE, a couple of papers have been publised including
https://doi.org/10.1103/PhysRevMaterials.6.114802
https://doi.org/10.1088/2053-1591/ac6ccc
https://doi.org/10.1063/5.0056172
https://doi.org/10.1063/1.5143038
I think that PHONOPY can also be combined with OpenMX.
https://phonopy.github.io/phonopy/
I hope that they help you.
Regards,
TO
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| Re: Phonon calculations ( No.4 ) |
- Date: 2022/12/05 16:31
- Name: Mehdi Vejdanihemmat <m.vejdanih@gmail.com>
- Dear Prof. Ozaki,
Great!!! I am very happy this day. I thought there was no interface between OpenMX and a phonon calculator. Thank you very much.
Best wishes,
Mehdi Vejdanihemmat
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| Re: Phonon calculations ( No.5 ) |
- Date: 2022/12/13 23:54
- Name: Mehdi Vejdanihemmat <m.vejdanih@gmail.com>
- Dear OpenMX users,
My displacement files number for phonon calculations is about 150. I use DFT+U. The
obtained displacement files atomic coordinates lack the flag "off" related to DFT+U
method while the original dat file has this flag for every coordinate. Could you
please tell me how can I correct the related code to consider this flag?
Thank you in advance,
Best wishes,
Mehdi Vejdanihemmat
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| Re: Phonon calculations ( No.6 ) |
- Date: 2022/12/14 23:52
- Name: Mehdi Vejdanihemmat <m.vejdanih@gmail.com>
- Hello,
I solved the mentioned problem.
Regards,
Mehdi Vejdanihemmat
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| Re: Phonon calculations ( No.7 ) |
- Date: 2023/01/05 01:37
- Name: Mehdi Vejdanihemmat <m.vejdanih@gmail.com>
- Hi everyone,
I got the following error in the last level of getting phonon dispersion. Can anyone help me to solve that?
[mehdi:12131] *** Process received signal ***
[mehdi:12131] Signal: Segmentation fault (11)
[mehdi:12131] Signal code: Address not mapped (1)
[mehdi:12131] Failing at address: 0x440000e8
[mehdi:12131] [ 0] /lib/x86_64-linux-gnu/libc.so.6(+0x43090)[0x14b5055b1090]
[mehdi:12131] [ 1] /home/mehdi/mambaforge/envs/alamode/lib/libmpi.so.40(PMPI_Comm_rank+0x37)[0x14b505994a37]
[mehdi:12131] [ 2] anphon(_ZN7PHON_NS5MyMPIC1EPNS_4PHONEi+0x10c)[0x561d76e62a2c]
[mehdi:12131] [ 3] anphon(_ZN7PHON_NS4PHONC1EiPPci+0x76)[0x561d76e7d416]
[mehdi:12131] [ 4] anphon(main+0x41)[0x561d76dd8891]
[mehdi:12131] [ 5] /lib/x86_64-linux-gnu/libc.so.6(__libc_start_main+0xf3)[0x14b505592083]
[mehdi:12131] [ 6] anphon(+0x2db79)[0x561d76dd8b79]
[mehdi:12131] *** End of error message ***
Segmentation fault (core dumped)
Thank you in advance,
Mehdi Vejdanihemmat
 |
| Re: Phonon calculations ( No.8 ) |
- Date: 2023/01/05 08:40
- Name: Masanobu Miyata <m-miyata@jaist.ac.jp>
- Hi.
Perhaps there is a problem with the compilation of ALAMODE. Compilation problems are complicated because they depend on the environment. I recommend that you use the easy installation method using conda, which is described on the official ALAMODE website. https://alamode.readthedocs.io/en/latest/install.html (Please see the session 3.2)
Best regards,
Miyata,
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| Re: Phonon calculations ( No.9 ) |
- Date: 2023/01/06 04:27
- Name: Mehdi Vejdanihemmat <m.vejdanih@gmail.com>
- Dear Dr. Miyata,
My installation method has been the easy installation method using conda. I have tried different ways to solve this problem but I have never succeeded yet. The phonon dispersion is the only thing that I need for my manuscript at this time. So, I would be thankful to you if you know a solution to guide me in this regard.
Best wishes,
Mehdi Vejdanihemmat
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| Re: Phonon calculations ( No.10 ) |
- Date: 2023/01/08 19:42
- Name: Mehdi Vejdanihemmat <m.vejdanih@gmail.com>
- Dear Prof. Ozaki,
You mentioned that PHONOPY can also be combined with OpenMX. Do you have any idea about how to do that?
Best regards,
Mehdi Vejdanihemmat
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| Re: Phonon calculations ( No.11 ) |
- Date: 2023/01/27 01:12
- Name: Mehdi Vejdanihemmat <m.vejdanih@gmail.com>
- Dear everyone,
One report:
I changed my ubuntu from 20.04 to 18.04 then my problem with alamode was solved!
Best regards,
Mehdi Vejdanihemmat
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| Re: Phonon calculations ( No.12 ) |
- Date: 2023/09/18 16:45
- Name: Arif <ariflukmantoro16@gmail.com>
- Dear Mehdi Vejdanihemmat,
I got some problem when I run the last step for calculating phonon dispersion using the anphon compiler. Have you found another solution to overcome this problem without downgrading the ubuntu series from 20.04 to 18.04?
Best Regards,
Arif
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Phonon calculations