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, 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 =========================================================
Hello Feng,
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.
The answer to your question lies in one of those cristallographic oddeness, namely that you can describe the crystallographic structure of quartz in two distinct sets of axis, the obverse (a,b,c) and the reverse (a', b', c), with the latter being obtained by rotation of the former by pi/3 around c. The caveat is that the cristalloraphic data you used are relevant to the reverse axes (and usually is described so in the litterature), whereas the P31 2 1 is relevant to the obverse. Thus you have to make a slight coordinate change; we had to deal with that before (Schlegel et al, Geochim. Cosmochim. Acta, vol. 66, p 3037, 2002), and we came up with the following cristallographic data P 32 2 1 a = 4.9137 b = 5.4047 x(O) = 0.5867 y(O) = 0.7328 Z(O) = 0.7855 x(Si) = 0.5303 y(Si) = 0 z(Si) = 2/3 As a structural check, all Si-O distances must be within 1.60-1.62 angstroms (160-162 pm for purists) Hope this will help; let me know if not Best regards, Michel
Oups - just a mistake; the unit cell coordinates are of course a=b = 4.9137 c = 5.4047 Sorry - Michel
participants (2)
-
Feng Wang
-
Michel Schlegel