Hi Bruce, Sorry, I was just using the different space group just to get the cluster to be oriented along the axes or at 45 degrees. With tetragonal symmetry, the cluster is oriented at 45 degrees with respect to the axes. If I don't use tetragonal symmetry, then the cluster is oriented as one might expect with respect to the axes. Raj's original question was about producing these two different orientations of the cluster, with one version of atoms produced the rotated and another the non-rotated. You investigated Raj's observation by running FEFF6. My point is more general, but still related to Raj's case in that, if the coordinates are rotated, a different result is obtained if one does a polarization-dependent FEFF6 calculation than if the coordinates are not rotated. So, Raj's observation of the rotation of the cluster with respect to the axes exposes an issue when running such a rotated cluster in FEFF6 with respect to POLARIZATION, versus a non-rotated cluster. NOTE: In FEFF6, one actually gets a different result (in the bct model I discussed) if one uses (100) versus (010) with the POLARIZATION card. This does not seem to happen for FEFF7. i.e. even for tetragonal symmetry, FEFF6 calculates some differences for orientations rotated by 90 degrees in-plane. As a convention, having the cluster oriented so that POLARIZATION agrees with axes does seem logical. For tetragonal symmetry, Demeter-Atoms seems to rotate the cluster. (I haven't checked hexagonal/trigonal) such that this does not appear to be the case. You could, instead of the bct example I used, work with just bcc Fe. In cubic, Demeter-Atoms generates a cluster in the feff.inp 0.00000 0.00000 0.00000 0 fe 0.00000 1.43300 1.43300 1.43300 1 fe.1 2.48203 -1.43300 1.43300 1.43300 1 fe.1 2.48203 1.43300 -1.43300 1.43300 1 fe.1 2.48203 -1.43300 -1.43300 1.43300 1 fe.1 2.48203 1.43300 1.43300 -1.43300 1 fe.1 2.48203 -1.43300 1.43300 -1.43300 1 fe.1 2.48203 1.43300 -1.43300 -1.43300 1 fe.1 2.48203 -1.43300 -1.43300 -1.43300 1 fe.1 2.48203 2.86600 0.00000 0.00000 1 fe.2 2.86600 -2.86600 0.00000 0.00000 1 fe.2 2.86600 0.00000 2.86600 0.00000 1 fe.2 2.86600 0.00000 -2.86600 0.00000 1 fe.2 2.86600 0.00000 0.00000 2.86600 1 fe.2 2.86600 0.00000 0.00000 -2.86600 1 fe.2 2.86600 and if one drops to tetragonal symmetry, same cell, same contents, just using lower symmetry for s&g, one obtains 0.00000 0.00000 0.00000 0 fe 0.00000 2.02657 0.00000 1.43300 1 fe.1 2.48203 -2.02657 0.00000 1.43300 1 fe.1 2.48203 0.00000 2.02657 1.43300 1 fe.1 2.48203 0.00000 -2.02657 1.43300 1 fe.1 2.48203 2.02657 0.00000 -1.43300 1 fe.1 2.48203 -2.02657 0.00000 -1.43300 1 fe.1 2.48203 0.00000 2.02657 -1.43300 1 fe.1 2.48203 0.00000 -2.02657 -1.43300 1 fe.1 2.48203 2.02657 2.02657 0.00000 1 fe.2 2.86600 -2.02657 2.02657 0.00000 1 fe.2 2.86600 2.02657 -2.02657 0.00000 1 fe.2 2.86600 -2.02657 -2.02657 0.00000 1 fe.2 2.86600 0.00000 0.00000 2.86600 1 fe.2 2.86600 0.00000 0.00000 -2.86600 1 fe.2 2.86600 which appears to be rotated 45 degrees with respect to the bcc variant, and if I drop down to orthorhombic (Immm), again, same cell 0.00000 0.00000 0.00000 0 fe 0.00000 1.43300 1.43300 1.43300 1 fe.1 2.48203 -1.43300 1.43300 1.43300 1 fe.1 2.48203 1.43300 -1.43300 1.43300 1 fe.1 2.48203 -1.43300 -1.43300 1.43300 1 fe.1 2.48203 1.43300 1.43300 -1.43300 1 fe.1 2.48203 -1.43300 1.43300 -1.43300 1 fe.1 2.48203 1.43300 -1.43300 -1.43300 1 fe.1 2.48203 -1.43300 -1.43300 -1.43300 1 fe.1 2.48203 2.86600 0.00000 0.00000 1 fe.2 2.86600 -2.86600 0.00000 0.00000 1 fe.2 2.86600 0.00000 2.86600 0.00000 1 fe.2 2.86600 0.00000 -2.86600 0.00000 1 fe.2 2.86600 0.00000 0.00000 2.86600 1 fe.2 2.86600 0.00000 0.00000 -2.86600 1 fe.2 2.86600 back to being apparently aligned as with the bcc...and so forth down to P1. So, for all but tetragonal, the orientation of the cluster can be identified with the orientation of the crystal axes. Does it not seem more logical to preserve the apparent orientation with respect to the crystal axes so that, when using POLARIZATION (issues in FEFF6 aside), confusion is less-likely? -R. On 12/21/2016 10:51 AM, Bruce Ravel wrote:
Robert,
You have me confused. You seem to be saying that using the correct space group symbol is important. I couldn't possibly disagree.
Raj's original question had to do with the fact that two different versions of atoms, which used different algorithms for interpreting the crystal data, resulted in clusters that were rotated relative to one another. My answer, appropriate (I think) in that case, was to shrug.
You seem to be commenting on something unrelated to the original question, but I'm not understanding the point.
B
On 12/21/2016 01:13 PM, Robert Gordon wrote:
Hi Bruce,
The atoms.inp file attached is for bct Fe. In symmetry I4/mmm, the resulting feff input has the coordinates rotated, while in Immm the resulting coordinates are not rotated relative to the crystal axes (i.e. in Immm the 2nd near neighbour is obvious as a lattice constant away in each direction).
So, with no polarization, the results for scattering paths are the same (using CRITERIA default), as expected Path # Degen Reff Scattering Path Type Rank I4/mmm Rank Immm 1 8 2.48 fe1 ss 100 100 2 4 2.835 fe2 ss 37.56 37.56 3 2 2.92 fe3 ss 17.59 17.59 4 16 3.897 fe1-fe1 ms 3.42 3.42 5 32 3.897 fe1-fe2 ms 12.83 12.83 7 16 3.94 fe1-fe3 ms 6.37 6.37
Now consider with POLARIZATION 1 0 0 (and 1 1 0 for I4/mmm)
# Degen Reff Scatt. Path Type I4 1 0 0 I4 1 1 0 Im 1 0 0
4 2.48 fe1 ss 100
4 2.48 fe1 ss 7.89
8 2.48 fe1 ss
100 100
4 2.835 fe2 ss 55.45
2 2.835 fe2 ss
62.05 62.05
16 3.897 fe1-fe1 ms 4.41 9.90 15.43
16 3.897 fe1- fe2 ms 19.03 21.58 21.59
For that first multiple scattering path, the scattering angles are 36.1/90 for I4(1 0 0), 55.1/55.1 for I4(110) and for Im(100) they are 55.1/124.9. The ranking of this path is not the same, and the plots for this path differ as well - in shape as well as amplitude.
Conceptually, the Immm model calculation has the atoms aligned with the crystal lattice and the I4/mmm has the atoms rotated. FEFF sees a difference, and I would take the Immm result as the correct one based on the positions of the atoms in the cluster relative to the axes.
-R.
On 12/21/2016 6:49 AM, Bruce Ravel wrote:
On 12/19/2016 11:01 PM, Robert Gordon wrote:
What if one were to do this FEFF calculation using the POLARIZATION card? 1 0 0 means something different if the atom positions have been rotated by 45 degrees relative to the crystal axes along which the polarization is defined.
Well ... you could rotate the polarization vector by 45 degrees ...
I guess I have always considered FEFF's polarization card to be an a posteriori addition to the feff.inp file -- i.e. a decision that the user makes after using Atoms to convert crystal data to a cluster in feff.inp.
B
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