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@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Feng Wang Sent: Saturday, February 18, 2006 2:28 AM To: ifeffit@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@phys.ualberta.ca Electron Microscopy Group Department of Physics University of Alberta ========================================================= _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit