I am using cif file for running DFT. The cif for spinel ferrites was obtained from Rietveld refinement of X-ray diffraction pattern. I am new could anyone help me understand what's wrong.
(1) I get a large number of atoms outside the crystal structure. Please see the
following picture. Is it normal? If not, what could be happening?
(2) Further when I run the programm, I get error message # 2070. I have
tried using "geom=nocrowd" but problem still remains the same. Please
look at the additional pictures.
Thanks for the help.
Dear Surender Kumar,
It looks like your problem is that you have different crystallographical setting conventions for the Rietveld refinement program and Gaussian. Two different positions of the origin are possible for the space group Fd-3m. These two positions are shifted with respect to each other at the vector (1/8;1/8;1/8). As a result, when you choose wrong origin, all atoms go into wrong positions. Particularly, 4 oxygen atoms appear almost exactly in the same place (distance ~0.15A) and you get "atoms too close" message. If Gaussian does not allow to change the setting, you have to add or subtract 0.125 to all coordinates in the cif file before using it for DFT.
Correct coordinates should be something like (0;0;0), (0.625; 0.625; 0.625), (0.38; 0.38; 0.38) for the setting 1 and (0.125; 0.125; 0.125), (0.5; 0.5; 0.5), (0.26; 0.26; 0.26) for the setting 2.
Thanks, Yes indeed that is correct. I got it right now. It's working well.Thanks again.
Hello,
I am new to DFT too, using Gaussian , i am trying to do a optimization of Pt2O,the statement of my problem is to used LANL2DZ for Pt and B3PW91 for O, my input file is
%chk=Pt2_O.chk
%mem=6MW
%nproc=1
# opt b3pw91/lanl2dz/ 6-311G(d) geom=connectivity
Title Card Required
0 3
O -0.63527963 -0.81827161 0.00000000
Pt -1.90279375 -2.16088606 0.00000000
Pt 0.60315437 -2.24995951 0.00000000
1 2 1.0 3 1.0
2 3 1.0
3
i get the error 2070 when i try, can anyone tell me what i am doing wrong ?
thanks for the answer but did you try it on your computer ? did it work ? i still receive the error message on mine , another question why don't you have the coordinate at the end ?
Thank you, it works now, although i don't have the error message anymore, i still need to modify the input file , i am supposed to calculate the adsorption energy of Pt2) and the methodology on the paper is little confusing, if you can take a look at it:
Methodology:
DFT as implemented in Gaussian9429 has been used for all
of the calculations. We employed the functional B3PW91, which
uses a combination of B330 exchange functionals and PW9131,32
correlation functionals. For Pt, the electrons from the 5s2, 5p6,
5d9, and 6s1 shells were treated explicitly using the Gaussian
(3s2p2d) basis set. The 1s to 4f core electrons were described
by the Los Alamos National Laboratory (LANL2DZ) using
effective core pseudopotentials of double-ê type.33 For oxygen
and hydrogen atoms, we used the polarized basis set 6-311G-
(d). The presence of a polarization d shell can ensure a possible
charge transfer from the substrate to the adsorbate.
Thank you again for your help
Article Computational Studies of the Interactions of Oxygen with Pla...
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