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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