[Ifeffit] Errors from Webatoms?
Barton, David (DG)
DGBarton at dow.com
Sat Feb 18 08:17:51 CST 2006
Feng,
Attached is a CIF file for alpha-SiO2 with the same space group (P3121) that you are attempting to use. The major difference that I see in this file compared with your input file is the Si location (0.465 0 1/3) vs. (-.465 .465 1/3). I am no crystallographer so I cannot tell you if a shift vector would make these equal, but this CIF file imports directly into Artemis and does give a 4-coordinate Si-O.
Dave
> -----Original Message-----
> From: ifeffit-bounces at millenia.cars.aps.anl.gov
> [mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf
> Of Feng Wang
> Sent: Saturday, February 18, 2006 2:28 AM
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] Errors from Webatoms?
>
>
> Hi everyone:
>
> I used WEBATOMS(version 1.8), to calculated the feff.inp for Si-K of
> alpha-SiO2 (quartz phase), using the crystal structure (as
> listed below)
> from Wyckoff's Crsytal Structures(P312-313), however, I could not get
> correct atomic configuration, such as, I did not get the
> tetrahedron (of 4
> nearest neighboring oxygen atoms), I got two n.n. oxygen
> atoms only, please
> refer to the results on the bottom.
> As suggested by Dr. Ravel, I tried the atoms in Artemis, but
> still I could
> not get correct feff.inp.Would you please help me to check
> and suggest,
> thank you so much.
>
> Best regards,
>
> Feng
>
> alpha-SiO2 crystal structure (from Wyckoff's book):
>
> hexagonal, a=4.91304, c=5.40463, space group: p3121 (#152).
> Si (3a): (-u,- u,1/3), (u,u,0) (0,u,2/3); O: (6c): (x,y,z),
> (y-x, -x, z+1/3), (-y, x-y,
> z+2/3), (x-y, -y,-z), (y,x,2/3-z), (-x,y-x,1/3-z). In which,
> z+u(si)=0.465,
> x=0.415, y=0.272, z=0.120.
>
> According to it, I used the input for WEBATOMS:
> Space group: p3121
> OUTPUT type: feff8.inp
> Edge: K
> shift: 0 0 0
> A=4.91304, c=5.40463
> Crystallographic Sites: Si (-0.465 -0.465, 1/3) O (0.415,
> 0.272, 0.12).
>
> And I got the atomic configuration in feff.inp as below:
>
> ATOMS * this list contains 449 atoms
> * x y z ipot tag distance
> 0.00000 0.00000 0.00000 0 Si 0.00000 0
> -0.51058 -0.99735 -1.15297 2 O 1.60771 1
> 0.21274 1.45917 -0.64854 2 O 1.61091 2
> 0.00000 0.00000 1.80158 1 Si 1.80158 3
> -2.27633 0.97033 0.00004 1 Si 2.47451 4
> 1.97849 -1.48619 0.00004 1 Si 2.47451 5
> 0.82118 -2.40002 0.64857 2 O 2.61822 6
> -1.11902 0.05650 -2.45008 2 O 2.69412 7
> 0.82118 2.51302 0.64857 2 O 2.72218 8
> -1.66789 1.91117 1.15301 2 O 2.78637 9
> 1.37005 -0.54535 2.45012 2 O 2.85964 10
> 2.58693 -0.54535 1.15301 2 O 2.88428 11
> -2.27633 0.97033 -1.80153 1 Si 3.06084 12
> -0.29784 2.45652 -1.80153 1 Si 3.06083 13
> 1.97849 -1.48619 -1.80153 1 Si 3.06083 14
> -0.29784 -2.45652 -1.80153 1 Si 3.06083 15
> -0.29784 2.45652 1.80154 1 Si 3.06084 16
> -0.29784 -2.45652 1.80154 1 Si 3.06084 17
> -1.11902 0.05650 2.95455 2 O 3.15987 18
> 1.37005 -0.54535 -2.95451 2 O 3.30206 19
> -3.43364 0.05650 0.64857 2 O 3.49481 20
> 0.21274 -3.45387 -0.64854 2 O 3.52066 21
> 0.00000 0.00000 -3.60305 1 Si 3.60305 22
> -1.66789 -3.00187 1.15301 2 O 3.62250 23
> 1.97849 3.42685 0.00004 1 Si 3.95698 24
> -0.51058 3.91569 -1.15297 2 O 4.11372 25
> 3.74424 1.45917 -1.15297 2 O 4.18065 26
> -4.04208 -0.99735 -0.64854 2 O 4.21352 27
> -2.88477 1.91117 2.45012 2 O 4.23999 28
> 3.95698 0.00000 -1.80153 1 Si 4.34778 29
> 1.97849 3.42685 -1.80153 1 Si 4.34778 30
> 3.95698 0.00000 1.80154 1 Si 4.34779 31
> -0.29784 2.45652 -3.60309 1 Si 4.37098 32
> -0.29784 -2.45652 -3.60309 1 Si 4.37098 33
> -2.27633 0.97033 3.60310 1 Si 4.37099 34
> -0.29784 2.45652 3.60310 1 Si 4.37099 35
> 1.97849 -1.48619 3.60310 1 Si 4.37099 36
> -0.29784 -2.45652 3.60310 1 Si 4.37099 37
> -0.51058 -0.99735 4.25166 2 O 4.39682 38
> -2.88477 1.91117 -2.95451 2 O 4.55012 39
> -2.27633 -3.94271 0.00004 1 Si 4.55265 40
> 4.46756 -0.99735 -0.64854 2 O 4.62325 41
>
>
>
>
> ==================================
> Feng Wang
> fwang at phys.ualberta.ca
> Electron Microscopy Group
> Department of Physics
> University of Alberta
> =========================================================
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