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Z2FH
Date: 2020/11/08 18:33
Name: Riemann Dearakhshan   <riemann.derakhshan@gmail.com>

Dear All,

Hope you are doing well.

After installing OpenMX and performing scf calculations, during the Z2 calculations, I git below error:

========================================================
./Z2FH Bi111-Z2.out <Z2FH.in > Z2FH.out
./Z2FH: error while loading shared libraries: libifcore.so.5: cannot open shared object file: No such file or directory
========================================================

I will highly appreciate it if you share your experience with me about where does this error comes and how I can fix it. Herewith I've also attached the list of libraries which is used for installation of the OpenMX.

Regards,
Riemann

========================================================
CC = mpiicc -O3 -xAVX -axCORE-AVX2 -ip -no-prec-div -qopenmp -I$EBROOTFFTW/include/fftw
FC = mpiifort -O3 -xAVX -axCORE-AVX2 -ip -no-prec-div -qopenmp
LIB= -L$EBROOTFFTW/lib -lfftw3 -L$MKLROOT/lib/intel64 -lmkl_scalapack_lp64 -lmkl_intel_lp64 -lmkl_blacs_intelmpi_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5 $
========================================================
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Re: Z2FH ( No.1 )
Date: 2020/11/08 22:28
Name: Naoya Yamaguchi

Hi,

If you use a supercomputer and you ran Z2FH by submitting batch jobs, you need to load such libraries on a calculation node.

Regards,
Naoya Yamaguchi
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Re: Z2FH ( No.2 )
Date: 2020/11/08 22:32
Name: Riemann Dearakhshan  <riemann.derakhshan@gmail.com>

Dear Naoya,

Thank yo so much for your prompt reply. I would ask which libraries should I load exactly?

Regards,
Riemann
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Re: Z2FH ( No.3 )
Date: 2020/11/09 01:54
Name: Naoya Yamaguchi

Dear Riemann,

There should be some convenient commands to load required libraries such as 'module' as you may have used it to build OpenMX, and you may find them from instructions of the system or ask the administrator about them.
Or, you can load the libraries manually if you know the location as follows.
https://sourceforge.net/p/lammps/mailman/message/22566255/

Regards,
Naoya Yamaguchi
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Re: Z2FH ( No.4 )
Date: 2020/11/10 22:23
Name: Riemann Dearakhshan  <riemann.derakhshan@gmail.com>

Dear Naoya,

While I'm running the Z2 sub-package for the Bi111 surface provided by OpenMX-3.9, I'm getting below error :
===========================
Error: Mismatch of the endianness
===========================
I will highly appreciate it if you guide me on how to fix it.

Regards,
Riemann
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Re: Z2FH ( No.5 )
Date: 2020/11/11 01:29
Name: Naoya Yamaguchi

Dear Riemann,

>./Z2FH Bi111-Z2.out <Z2FH.in > Z2FH.out

If you run Z2FH like that, you can get such errors.
You should specify an SCFOUT file to run Z2FH as follows.
$ ./Z2FH Bi111-Z2.scfout <Z2FH.in > Z2FH.out

Regards,
Naoya Yamaguchi
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Re: Z2FH ( No.6 )
Date: 2020/11/17 05:29
Name: Riemann Dearakhshan  <riemann.derakhshan@gmail.com>

Dear Naoya Yamaguchi,

I'm wondering for the case of 2D materials, which nu from the list (nu0,nu1,nu2,nu3) I haave to consider to judge if the it is in topological phase or not?

Regards,
Riemann
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Re: Z2FH ( No.7 )
Date: 2020/11/17 17:36
Name: Hikaru Sawahata  <sawahata@cphys.s.kanazawa-u.ac.jp>

Dear Riemann,

Thank you for using my code, I'm Hikaru Sawahata in Kanazawa university.

Please see the manual of Z2FH.
http://www.openmx-square.org/openmx_man3.9/node187.html

In case of 2D materials, nu3 is topological number of the system if you set the vacuum region in z direction.
In addition, if nu0 and nu1 and nu2 are zero in 2D materials, your calculation may be correct.

Regards,
Hikaru Sawahata
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Re: Z2FH ( No.8 )
Date: 2020/11/17 18:32
Name: Riemann Dearakhshan  <riemann.derakhshan@gmail.com>

Dear Hikaru Sawahata

Hope you are doing well.
In my case nu0 and nu1 and nu2 are zero and only nu3 is equal to one as below
================================================================
(x0,xpi,y0,ypi,z0,zpi)=(0.000000,0.000000,-0.000000,0.000000,1.000000,1.000000)
Z2 invariant:(nu0,nu1,nu2,nu3):(0,0,0,1)
================================================================
So, In according to you previous post can say it is in topological phase yes?

Regards,
Riemann
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Re: Z2FH ( No.9 )
Date: 2020/11/17 19:12
Name: Hikaru Sawahata  <sawahata@cphys.s.kanazawa-u.ac.jp>

Dear Riemann,

Yes, Bi(111) is a topological insulator.
>So, In according to you previous post can say it is in topological phase yes?
Please see my article's introduction.
https://iopscience.iop.org/article/10.7567/JJAP.57.030309

If it is not topological, nu3 becomes 0.

Hikaru Sawahata
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Re: Z2FH ( No.10 )
Date: 2020/11/17 19:23
Name: Riemann Dearakhshan  <riemann.derakhshan@gmail.com>

Dear Hikaru Sawahata,

I highly appreciate your prompt and helpful reply.

Regarding your paper, it sounds interesting and useful and I will go through it as soon as possible. I'm also wondering if it is possible to reproduce evolution of the Wannier charge centers (Fig.3 of your paper) based on the OpenMX outputs?

Regards,
Vahid
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Re: Z2FH ( No.11 )
Date: 2020/11/18 18:10
Name: Hikaru Sawahata  <sawahata@cphys.s.kanazawa-u.ac.jp>

Dear Riemann,

The code of computing 1D Wannier function center is not included in OpenMX yet.
I wrote the Figure 3 by using Dr. Yamaguchi's code.
https://github.com/Ncmexp2717/HWC
If you want to create WFC figures, you have to modify it to output the value of "wfcAB" arrays.

Hikaru Sawahata
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