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formate of seed_name.AtomMulP genrated by kSpin
Date: 2019/12/17 19:43
Name: Umar farooq   <farooqmu@sustech.edu.cn>

I want to do some analyses on the magnetic moment, I know I can use MulPCalc and can provide can get atomic contribution of spin moments. However I want to get contribution with a specific K-point.
I need to understand the format of "seed_name_.AtomMulP" file generated by the program "kSpin".

If I can get any help I will really appreciate.



Thanks


M. Umar Farooq

Southern University of Science and Technology
Department of Physics

1088 Xueyuan Avenue, Nanshan District, Shenzhen, Guangdong

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Re: formate of seed_name.AtomMulP genrated by kSpin ( No.1 )
Date: 2019/12/18 01:22
Name: Naoya Yamaguchi

Hi,

>However I want to get contribution with a specific K-point.

Please use "MulPOnly" and "MulPCalc".
http://www.openmx-square.org/openmx_man3.9/node179.html
http://www.openmx-square.org/openmx_man3.9/node180.html
And "MulPCalc" is just a script and enables you to get the expectation values of Pauli matrices.

You may find the format by referring to the following and checking "fscanf":
https://github.com/Ncmexp2717/SOField/blob/master/MulPCalc.c

And, I leave it as follows shortly in the case of "MulPOnly":
l.1 Data_size Atom_Num
l.2 k_x, k_y, k_z, {state, energy, Re(alpha-alpha), Re(beta-beta), Re(alpha-beta), Im(alpha-beta)}, {...}, {...}, ..., {...} <- # of {...} = "Atom_Num"
l.3 k_x, k_y, k_z, {state, energy, Re(alpha-alpha), Re(beta-beta), Re(alpha-beta), Im(alpha-beta)}, {...}, {...}, ..., {...}
.
.
.
l.(n+1) k_x, k_y, k_z, {state, energy, Re(alpha-alpha), Re(beta-beta), Re(alpha-beta), Im(alpha-beta)}, {...}, {...}, ..., {...}
<- where n = "Data_size".

Regards,
Naoya Yamaguchi
メンテ
Re: formate of seed_name.AtomMulP genrated by kSpin ( No.2 )
Date: 2019/12/18 20:57
Name: Arqum Hashmi

Dear Nagoya Yamaguchi

I have tried to calculate it as you suggested. But the format of 'kpoint.in' file is vague.

In manual, it is mentioned that the file 'kpoint.in' is stored in the directory 'work'. But i did not find any 'kpoint.in' file in work directory. Can you please provide the sample file for 'kpoint.in'.





University of Tsukuba&#160;1-1-1 Tennodai, Tsukuba, Ibaraki 305-8577, Japan
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Re: formate of seed_name.AtomMulP genrated by kSpin ( No.3 )
Date: 2019/12/19 03:11
Name: Naoya Yamaguchi

Dear Arqum Hashmi,

Thank you for your comment.
As you pointed it out, "kpoint.in" is not included in directory "work". I would ask Prof. Ozaki to include it into a patch.

I leave the format of "kpoint.in" as below:
l.1 N <- # of sets of a k-point of (k_x, k_y, k_z) and a state of nu
l.2 k_x, k_y, k_z, nu <- the 1st set of a k-point and a state
l.3 k_x, k_y, k_z, nu <- the 2nd set of a k-point and a state
.
.
.
l(N+1) k_x, k_y, k_z, nu <- the Nth set of a k-point and a state

And, the following bash script is the correct one to prepare an example of "kpoint.in" for an example of an Au(111) surface introduced in http://www.openmx-square.org/openmx_man3.9/node179.html:
.
% rm -f kpoint.in && awk '{for (i=0; i<$1; i++){printf "%17.14f %17.14f %17.14f %d\n", 0, $2*cos(2*atan2(0, -1)/$1*i), $2*sin(2*atan2(0, -1)/$1*i), $3 >> "buffer"}; sum+=$1; if (!$1) {print sum; exit}}' - > N.in && cat N.in buffer >> kpoint.in && rm N.in buffer

After that, if you give values as follows:
40 0.18 55 <- # of k-points; radius; state (band index) (outer circle in k-space)
40 0.15 56 <- # of k-points; radius; state (band index) (inner circle in k-space)
0 <- exit
, you get "kpoint.in" and you can see the content of "kpoint.in" as follows:
% cat kpoint.in
80
0.00000000000000 0.18000000000000 0.00000000000000 55
0.00000000000000 0.17778390130712 0.02815820370724 55
0.00000000000000 0.17119017293313 0.05562305898749 55
0.00000000000000 0.16038117435391 0.08171828995312 55
0.00000000000000 0.14562305898749 0.10580134541265 55
0.00000000000000 0.12727922061358 0.12727922061358 55
0.00000000000000 0.10580134541265 0.14562305898749 55
0.00000000000000 0.08171828995312 0.16038117435391 55
0.00000000000000 0.05562305898749 0.17119017293313 55
0.00000000000000 0.02815820370724 0.17778390130712 55
0.00000000000000 0.00000000000000 0.18000000000000 55
0.00000000000000 -0.02815820370724 0.17778390130712 55
0.00000000000000 -0.05562305898749 0.17119017293313 55
0.00000000000000 -0.08171828995312 0.16038117435391 55
0.00000000000000 -0.10580134541265 0.14562305898749 55
0.00000000000000 -0.12727922061358 0.12727922061358 55
0.00000000000000 -0.14562305898749 0.10580134541265 55
0.00000000000000 -0.16038117435391 0.08171828995312 55
0.00000000000000 -0.17119017293313 0.05562305898749 55
0.00000000000000 -0.17778390130712 0.02815820370724 55
0.00000000000000 -0.18000000000000 0.00000000000000 55
0.00000000000000 -0.17778390130712 -0.02815820370724 55
0.00000000000000 -0.17119017293313 -0.05562305898749 55
0.00000000000000 -0.16038117435391 -0.08171828995312 55
0.00000000000000 -0.14562305898749 -0.10580134541265 55
0.00000000000000 -0.12727922061358 -0.12727922061358 55
0.00000000000000 -0.10580134541265 -0.14562305898749 55
0.00000000000000 -0.08171828995312 -0.16038117435391 55
0.00000000000000 -0.05562305898749 -0.17119017293313 55
0.00000000000000 -0.02815820370724 -0.17778390130712 55
0.00000000000000 -0.00000000000000 -0.18000000000000 55
0.00000000000000 0.02815820370724 -0.17778390130712 55
0.00000000000000 0.05562305898749 -0.17119017293313 55
0.00000000000000 0.08171828995312 -0.16038117435391 55
0.00000000000000 0.10580134541265 -0.14562305898749 55
0.00000000000000 0.12727922061358 -0.12727922061358 55
0.00000000000000 0.14562305898749 -0.10580134541265 55
0.00000000000000 0.16038117435391 -0.08171828995312 55
0.00000000000000 0.17119017293313 -0.05562305898749 55
0.00000000000000 0.17778390130712 -0.02815820370724 55
0.00000000000000 0.15000000000000 0.00000000000000 56
0.00000000000000 0.14815325108927 0.02346516975603 56
0.00000000000000 0.14265847744427 0.04635254915624 56
0.00000000000000 0.13365097862826 0.06809857496093 56
0.00000000000000 0.12135254915624 0.08816778784387 56
0.00000000000000 0.10606601717798 0.10606601717798 56
0.00000000000000 0.08816778784387 0.12135254915624 56
0.00000000000000 0.06809857496093 0.13365097862826 56
0.00000000000000 0.04635254915624 0.14265847744427 56
0.00000000000000 0.02346516975603 0.14815325108927 56
0.00000000000000 0.00000000000000 0.15000000000000 56
0.00000000000000 -0.02346516975603 0.14815325108927 56
0.00000000000000 -0.04635254915624 0.14265847744427 56
0.00000000000000 -0.06809857496093 0.13365097862826 56
0.00000000000000 -0.08816778784387 0.12135254915624 56
0.00000000000000 -0.10606601717798 0.10606601717798 56
0.00000000000000 -0.12135254915624 0.08816778784387 56
0.00000000000000 -0.13365097862826 0.06809857496093 56
0.00000000000000 -0.14265847744427 0.04635254915624 56
0.00000000000000 -0.14815325108927 0.02346516975603 56
0.00000000000000 -0.15000000000000 0.00000000000000 56
0.00000000000000 -0.14815325108927 -0.02346516975603 56
0.00000000000000 -0.14265847744427 -0.04635254915624 56
0.00000000000000 -0.13365097862826 -0.06809857496093 56
0.00000000000000 -0.12135254915624 -0.08816778784387 56
0.00000000000000 -0.10606601717798 -0.10606601717798 56
0.00000000000000 -0.08816778784387 -0.12135254915624 56
0.00000000000000 -0.06809857496093 -0.13365097862826 56
0.00000000000000 -0.04635254915624 -0.14265847744427 56
0.00000000000000 -0.02346516975603 -0.14815325108927 56
0.00000000000000 -0.00000000000000 -0.15000000000000 56
0.00000000000000 0.02346516975603 -0.14815325108927 56
0.00000000000000 0.04635254915624 -0.14265847744427 56
0.00000000000000 0.06809857496093 -0.13365097862826 56
0.00000000000000 0.08816778784387 -0.12135254915624 56
0.00000000000000 0.10606601717798 -0.10606601717798 56
0.00000000000000 0.12135254915624 -0.08816778784387 56
0.00000000000000 0.13365097862826 -0.06809857496093 56
0.00000000000000 0.14265847744427 -0.04635254915624 56
0.00000000000000 0.14815325108927 -0.02346516975603 56

And no results of the test calculation are shown, and I guess that a figure showing it is omitted.
I am sorry for inconvenience due to wrong information in the manual and also plan to modify it.

For example, if you want to calculate it for state 10 on gamma-point, the following is such an example of "kpoint.in":
1
0.0 0.0 0.0 10

Regards,
Naoya Yamaguchi
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Re: formate of seed_name.AtomMulP genrated by kSpin ( No.4 )
Date: 2019/12/19 18:44
Name: Arqum Hashmi  <hashmi.arqum.ga@u.tsukuba.ac.jp>

Dear Nagoya Yamaguchi
Thanks a lot for your detailed explanation.

I have just tried to test the example using the kpoint.in file you made. But even after calculation finished, it didn't generate any Au111Surface_MO.MulP_* files. The calculation didn't give any error as well.


This is the output

******************************************************************
******************************************************************
kSpin:
code for evaluating spin related properties
in momentum space of solid state materials.
Copyright (C), 2019,
Hiroki Kotaka, Naoya Yamaguchi and Fumiyuki Ishii.
This software includes the work that is distributed
in version 3 of the GPL (GPLv3).

Please cite the following article:
H. Kotaka, F. Ishii, and M. Saito,
Jpn. J. Appl. Phys. 52, 035204 (2013).
DOI: 10.7567/JJAP.52.035204.
******************************************************************
******************************************************************


Input filename is "Au111Surface.scfout"


Read the scfout file (Au111Surface.scfout)
***
The file format of the SCFOUT file: 3
And it supports the following functions:
- jx
- polB
- kSpin
- Z2FH
- calB
***

Start "MulPOnly" Calculation (6).

########### ORBITAL DATA ##################
ClaOrb_MAX[0]: 2
ClaOrb_MAX[1]: 8
Total Band (2*n): 124
###########################################

############ CALC TIME ####################
Total Calculation Time: 1.835213 (s)
###########################################


I am wondering what the problem could be?? Any guidance and suggestions would be appreciated.

Thanks and Regards
Arqum Hashmi
Center for Computational Sciences, University of Tsukuba
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Re: formate of seed_name.AtomMulP genrated by kSpin ( No.5 )
Date: 2019/12/20 02:24
Name: Naoya Yamaguchi

Dear Arqum Hashmi,

The following is an example of standard output:

******************************************************************
******************************************************************
kSpin:
code for evaluating spin related properties
in momentum space of solid state materials.
Copyright (C), 2019,
Hiroki Kotaka, Naoya Yamaguchi and Fumiyuki Ishii.
This software includes the work that is distributed
in version 3 of the GPL (GPLv3).

Please cite the following article:
H. Kotaka, F. Ishii, and M. Saito,
Jpn. J. Appl. Phys. 52, 035204 (2013).
DOI: 10.7567/JJAP.52.035204.
******************************************************************
******************************************************************


Input filename is "Au111Surface.scfout"


Start "MulPOnly" Calculation (6).

########### ORBITAL DATA ##################
ClaOrb_MAX[0]: 2
ClaOrb_MAX[1]: 8
Total Band (2*n): 124
###########################################

############ CALC TIME ####################
Total Calculation Time: 0.642631 (s)
###########################################
############ CALC TIME ####################
Total Calculation Time: 0.660566 (s)
###########################################

Your output looks to include only single "CALC TIME", but I think that there should appear it twice if the calculation is normal.
Have you added "80" into the beginning of "kpoint.in"?
If not, "MulPOnly" may receive 0 as a value of the number of sets because the first column of the first set is "0.00000000000000".
Could you check the beginning of "kpoint.in"?

>I am wondering what the problem could be?
"MulPOnly" can calculate k-space spin density matrices on given k-points.
For more detail, please refer to the following:
http://www.openmx-square.org/tech_notes/note_kSpin-1_0.pdf

Regards,
Naoya Yamaguchi
メンテ
Re: formate of seed_name.AtomMulP genrated by kSpin ( No.6 )
Date: 2019/12/20 12:41
Name: Naoya Yamaguchi

Dear Arqum Hashmi,

Although you may find a binary named "MulPOnly", please run "kSpin" using an input file with "Calc.Type=MulPOnly".
The binary "MulPOnly" is included in the recipe of makefile, but it was prepared before uniting it to "kSpin".
I would also ask him to delete some unimportant recipes including it.

Regards,
Naoya Yamaguchi
メンテ
Re: formate of seed_name.AtomMulP genrated by kSpin ( No.7 )
Date: 2019/12/21 18:33
Name: Arqum Hashmi  <hashmi.arqum.ga@u.tsukuba.ac.jp>

Dear Nagoya Yamaguchi
Thank you so much for your help and a thorough explanation.

I think it isn't a problem of kpoint.in nor the binary "MulPOnly". I have only used kSpin. As i explained before when i run the calculation, it ended only withonly single "CALC TIME" without any error.

I have tried to run the kSpin in serial and then i got an error msg



Start "MulPOnly" Calculation (6).

########### ORBITAL DATA ##################
ClaOrb_MAX[0]: 2
ClaOrb_MAX[1]: 8
Total Band (2*n): 124
###########################################

Fatal error in PMPI_Bcast: Invalid root, error stack:
PMPI_Bcast(2654): MPI_Bcast(buf=0x15736b0, count=0, MPI_DOUBLE, root=4, MPI_COMM
PMPI_Bcast(2608): Invalid root (value given was 4)
[unset]: write_line error; fd=-1 buf=:cmd=abort exitcode=336151303
:
system msg for write_line failure : Bad file descriptor


Is it the problem of installation?? So far everything is running fine except this kSpin with "Calc.Type=MulPOnly".

メンテ
Re: formate of seed_name.AtomMulP genrated by kSpin ( No.8 )
Date: 2019/12/23 12:02
Name: Naoya Yamaguchi

Dear Arqum Hashmi,

Thank you for reporting the error because I got to find the cause soon.
I leave a revised file "MulPOnly.c" in the following:
https://gist.github.com/Ncmexp2717/30cd5b05f1e2167f25ecef06a3bd6546
And, could you try it?

I also leave an example of a calclation and a visualization of it as follows:
$ mpirun ./kSpin Au111Surface_MO.dat
$ ./MulPCalc Au111Surface_MO.dat
$ gnuplot Au111Surface_MO_MC.plotexample

After that, you may find a spin texture of an Au(111) surface.

Regards,
Naoya Yamaguchi
メンテ
Re: formate of seed_name.AtomMulP genrated by kSpin ( No.9 )
Date: 2019/12/23 15:31
Name: Arqum Hashmi  <hashmi.arqum.ga@u.tsukuba.ac.jp>

Dear Nagoya Yamaguchi

You have figured it perfectly and the problem is soved now.

Thank you so much for your great help.
メンテ
Re: formate of seed_name.AtomMulP genrated by kSpin ( No.10 )
Date: 2019/12/31 03:15
Name: Umar farooq  <farooqmu@sustech.edu.cn>

Dear,

please can you tell me the units of k_x, k_y, k_z in kpoint.in? is it (1/Å) or scaled units ?



thanks

M. Umar Farooq

Southern University of Science and Technology
Department of Physics
メンテ
Re: formate of seed_name.AtomMulP genrated by kSpin ( No.11 )
Date: 2019/12/31 11:57
Name: Naoya Yamaguchi

Dear M. Umar Farooq,

The unit of k_x, k_y, k_z in "kpoint.in" is a.u., that is, Bohr^(-1).

Regards,
Naoya Yamaguchi
メンテ

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