rprim and spacegroup

elia · Post by **elia** » Sun Feb 17, 2019 6:43 pm

gs.out: optimization of the cell geometry; (45.68 KiB) Downloaded 299 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

ebousquet · Post by **ebousquet** » Thu Feb 21, 2019 5:21 pm

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:

Code: Select all

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

elia · Post by **elia** » Thu Feb 21, 2019 8:09 pm

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

ebousquet · Post by **ebousquet** » Tue Feb 26, 2019 3:48 pm

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

anhhv · Post by **anhhv** » Thu Feb 28, 2019 4:18 am

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.

elia · Post by **elia** » Thu Feb 28, 2019 4:38 am

Hi Anh,
Thanks a lot for the reply,,, I will try that
Regards,
Elia.

ABINIT Discussion Forums

rprim and spacegroup [SOLVED]

rprim and spacegroup

Re: rprim and spacegroup

Re: rprim and spacegroup

Re: rprim and spacegroup

Re: rprim and spacegroup

Re: rprim and spacegroup [SOLVED]