ABINIT Discussion Forums

Hello,everyone
After finishing the tutorial lessons,i try to do some excirses a litte more diffcult. During the process, some confuses comeing up.like the varible Xred.
In a article(Phys.Rev. B 65, 214302. 2002),it said " in the hexagonal coordinates, the atoms in LiNiO3 of paraelectric phase like follows:
Ni (0,0,0)
Li (0,0,1/4)
O1 (-1/3,-1/3+x,7/12)
O2 (1/3-x,-x,7/12)
O3 (x,1/3,7/12)"
i am wondering how these informations represetns in the input files. As far as i know,the varibles Rprim and Xred to decide the atoms postions,then how the hexagonal coordinates and the x in the above article to represent in these two varibles.
Thanks for your attation, i will be very aprreciate if you can reply me.
Best regards



from Xiaole Zhang

Dear Xiaole Zhang,

hexagonal structure is much easier (than rprim) to input using

angdeg 90 90 120

and the xreds of the atoms you mention are given as described here http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/varbas.html#xred.
"x" is a free coordinate and it's value is probably mentioned somewhere in that refrence paper you have. This value you should add or subtract from the rationales given in the atomic reduced coordinates. For example, if the x=0.12, then the O2 coordinated would be (0.213333333333,-0.12,7/12).

Cheers!

Igor Lukacevic

Very appreciate your reply, very useful for me.Thank you very much.

Dear lgor Lukacevic
i used the method you mentioned above,but still have some problems.
This is my input file
ngkpt 6 6 6 # In the present example, only this grid of k points is considered
# A full convergence study on k points should be done, see the above lines.

#Definition of the unit cell
#**********************************
acell 9.688 9.688 25.611
angdeg 90 90 120

#Definition of the atoms
#*********************
natom 5
ntypat 3
znucl 28 3 8
typat 1 2 3 3 3
xred 0 0 0
0 0 0.25
-0.3333 -0.2913 0.5833
0.2913 -0.0420 0.5833
0.0420 0.3333 0.5833
ixc 3

#Definition of the scf procedure
#******************************
iscf 5
nstep 1000

#Definition of the plane wave basis
#************************************
ecut 45
ecutsm 0.5
dilatmx 1.05

nshiftk 1
shiftk 0.5 0.5 0.5

#Structural relaxation
#*********************
ionmov 3
optcell 1
tolvrs 1.0d-15
tolmxf 5.0d-5
ntime 100

# add to conserve old < 6.7.2 behavior for calculating forces at each SCF step
optforces 1
After running the code , the log file have the error
symlatt : the Bravais lattice is hP (primitive hexagonal)
xred is defined in input file
ingeo : takes atomic coordinates from input array xred

symlatt : the Bravais lattice is hP (primitive hexagonal)

symlatt : the Bravais lattice is hP (primitive hexagonal)
symspgr : the symmetry operation no. 1 is the identity
symaxes : the symmetry operation no. 2 is a 3-axis
symaxes : the symmetry operation no. 3 is a 3-axis
symspgr : spgroup= 143 P3 (=C3^1)
getkgrid : length of smallest supercell vector (bohr)= 5.812800E+01
Simple Lattice Grid
symkpt : found identity, with number 1

symkpt: ERROR -
Chksymbreak=1 . It has been observed that the k point grid is not symmetric :
for the symmetry number 2
with symrc1= -1 1 0 -1 0 0 0 0 1
the symmetric of the k point number 211 with components 8.333333E-02 -8.333333E-02 -8.333333E-02
does not belong to the k point grid.
Please, read carefully the description of the input variable chksymbreak,
Then, you might switch it to zero, or change your k point grid to one that is symmetric.
and the symspgr=143 P3 mentioned in log file is the space group of my system? but the system i want is 167 R3c,i am confused with that.
wish you reply me, thank you in advanced.

ilukacevic wrote:Dear Xiaole Zhang,

hexagonal structure is much easier (than rprim) to input using

angdeg 90 90 120

and the xreds of the atoms you mention are given as described here http://www.abinit.org/documentation/helpfiles/for-v5.8/input_variables/varbas.html#xred.
"x" is a free coordinate and it's value is probably mentioned somewhere in that refrence paper you have. This value you should add or subtract from the rationales given in the atomic reduced coordinates. For example, if the x=0.12, then the O2 coordinated would be (0.213333333333,-0.12,7/12).

Cheers!

Igor Lukacevic

Hello,

For hexagonal systems, you cannot use shiftk 0.5 0.5 0.5, except if you ask abinit not to take into account symmetries. You can find information about shiftk here :
http://www.abinit.org/documentation/helpfiles/for-v6.8/input_variables/varbas.html#shiftk

Also an visual explanation is given here for the hexagonal symmetry and allowed shiftk values :
http://forum.abinit.org/viewtopic.php?f=8&t=3

In short : change shiftk 0.5 0.5 0.5 to shiftk 0.0 0.0 0.5

David