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rprim and spacegroup
Posted: Sun Feb 17, 2019 6:43 pm
by elia
gs.out- optimization of the cell geometry
- (45.68 KiB) Downloaded 298 times
Dear all,
After full optimization of the cell geometry (using optcell=2 and ionmov=2), I have obtained gs.out file. How can I determine the rprim and spacegroup?
Thanks a lot.
Best,
Elia
Re: rprim and spacegroup
Posted: Thu Feb 21, 2019 5:21 pm
by ebousquet
Dear Elia,
At the beginning of your output you have the following line:
Code: Select all
Symmetries : space group P3 m 1 (#156); Bravais hP (primitive hexag.)
Then for each relaxation steps you have at some point the following informations regarding the cell:
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Scale of Primitive Cell (acell) [bohr]
7.54115899680355E+00 7.54115899680355E+00 4.54864865841844E+01
Real space primitive translations (rprimd) [bohr]
5.33240466464574E+00 0.00000000000000E+00 5.33240466464574E+00
5.33240466464574E+00 5.33240466464574E+00 -2.20271039884021E-32
-1.69152729509060E-01 3.21635807173835E+01 3.21635807173835E+01
Unitary Cell Volume (ucvol) [Bohr^3]= 1.83392299319453E+03
Angles (23,13,12)= [degrees]
6.01740460805992E+01 6.01740460805992E+01 6.00000000000000E+01
Lengths [Bohr]
7.54115899680355E+00 7.54115899680355E+00 4.54864865841844E+01
which, I think, is what you are looking for.
Best wishes,
Eric
Re: rprim and spacegroup
Posted: Thu Feb 21, 2019 8:09 pm
by elia
Dear Eric,
Thank you for your answer. In order to obtain rprim, I have used rprim(i,j) = rprimd(i,j)/acell(j).
:::::::::::::::::::::::::::::::::::::::::::::::::::
acell (Bohr) 7.54 7.54 45.486
rprimd
5.33 0.0 5.33
5.33 5.33 0.0
-0.16915 32.163 32.163
rprim
0.707106 0.0 0.11723
0.707106 0.707106 0.0
-0.0224 4.265 0.70710189
::::::::::::::::::::::::::::::::::::::::::::::::::::::
But, the calculated rprim leads to space group p 1 (triclinic). How can I calculate the correct rprim?
Best wishes,
Elia
Re: rprim and spacegroup
Posted: Tue Feb 26, 2019 3:48 pm
by ebousquet
Dear Elia,
It could be related to the number of digit at which the symmetries are detected (tolsym) is higher than the number of digits at which your rprim is rounded... You can check by reducing the tolsym flag.
Best wishes,
Eric
Re: rprim and spacegroup
Posted: Thu Feb 28, 2019 4:18 am
by anhhv
Hi Elia,
Have you tried to use python-based tool named abipy
https://github.com/abinit/abipy. When it is installed, if you are in a terminal (e.g. in Linux), simply use command ``abiopen.py + name of file'' you want to extract information. This will lead you to an ipython-environment with an object called abifile. From that, you can get many things you need. For instance,
abiopen.py your_file_name.GSR.nc
nkpt = abifile.nkpt
kpoints = abifile.kpoints
eband = abifile.ebands
fermie = eband.fermie
struct = eband.structure
spg = struct.abi_spacegroup
symrec = spg.symrec
Best,
Anh.
Re: rprim and spacegroup [SOLVED]
Posted: Thu Feb 28, 2019 4:38 am
by elia
Hi Anh,
Thanks a lot for the reply,,, I will try that
Regards,
Elia.