[Ifeffit] more bugs in atoms?
George Sterbinsky
GeorgeSterbinsky at u.northwestern.edu
Thu May 12 16:30:58 CDT 2011
Hi Lisa,
I'm not very familiar with PbSO4, so I'm not sure if I can help, but your
email immediately brought some questions to mind.
First, did you import the same information into atoms and the crystal
structure program? The way you worded your message made me think that the
crystal structure program already "knew" the structure of PbSO4, in which
case perhaps it is using a structure that is slightly different from the one
you import into atoms.
Second, what is the source of the structure data you are feeding into atoms?
In my experience, errors and inconsistencies in the reporting of structure
data in the literature can lead to unusual results in atoms.
Best,
George
On Wed, May 11, 2011 at 3:07 PM, Gudrun Lisa Bovenkamp <
bovenkamp at physik.uni-bonn.de> wrote:
> Hey everybody,
>
> For a while I was wondering why I could not get a proper XANES simulation
> using FEFF (8 or 9). Recently I realized that the xyz list which is created
> in atoms from the crystal structure is not the same as from a crystal
> structure program for PbSO4. Can somebody please check this. I attached my
> feff.imp file including the atoms.imp (which was created by arthemis).
>
> Thanks,
> Lisa
>
>
> * input file was generated by Artemis 0.8.014
> * Atoms written by and copyright (c) Bruce Ravel, 1998-2001
>
> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
> * total mu*x=1: 13.94 microns, unit edge step: 24.69 microns
> * specific gravity = 5.382
> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
> * Normalization correction: 0.00039 ang^2
> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
>
> * -----------------------------------------------------------------
> * The following crystallographic data were used:
> *
> * title *-PbSO4 -[PNMA] Anglesite - orthorhombic
> * title 'James, R W'
> * title Proceedings of the Royal Society of London, Series A:
> Mathematical and Physical Sciences (76,1906-)
> * space = P n m a
> * a = 8.450 b = 5.380 c = 6.930
> * alpha = 90.0 beta = 90.0 gamma = 90.0
> * core = Pb edge = L3
> * atoms
> * ! elem x y z tag occ
> * Pb 0.31530 0.25000 0.33750 1.00000
> * S 0.44300 0.25000 -0.19470 1.00000
> * O -1.00000 -1.00000 -1.00000 1.00000
> * -----------------------------------------------------------------
>
> EDGE L3
> S02 1.0
> CONTROL 1 1 1 1 1 1
> PRINT 1 0 0 0 0 0
> SCF 5.16556 0 15 0.1
> EXCHANGE 0 0 0
> XANES 6.0 0.07 0.5
> FMS 6
>
> *LDOS -20 20 0.1
> POTENTIALS
> * ipot z [ label l_scmt l_fms stoichiometry ]
> 0 82 Pb -1 -1 0
> 1 8 O -1 -1 1
> 2 16 S -1 -1 1
> 3 82 Pb -1 -1 1
>
>
> ATOMS * this list contains 156 atoms
> * x y z ipot tag distance
> 0.00000 0.00000 0.00000 0 Pb 0.00000
> 1.56072 1.34500 1.12613 3 O_1 2.34799
> 1.56072 -1.34500 1.12613 3 O_1 2.34799
> 1.07906 0.00000 3.24185 2 S_1 3.41672
> -2.18263 2.69000 -0.22315 2 S_2 3.47128
> -2.18263 -2.69000 -0.22315 2 S_2 3.47128
> 2.04237 2.69000 -0.98960 2 S_3 3.51947
> 2.04237 -2.69000 -0.98960 2 S_3 3.51947
> -2.66429 1.34500 -2.33887 3 O_2 3.79180
> -2.66429 -1.34500 -2.33887 3 O_2 3.79180
> 1.07906 0.00000 -3.68815 2 S_4 3.84276
> -3.14594 0.00000 2.47540 2 S_5 4.00307
> 4.22500 0.00000 -1.21275 1 Pb_1 4.39561
> -4.22500 0.00000 -1.21275 1 Pb_1 4.39561
> 1.56072 4.03500 1.12613 3 O_3 4.47049
> 1.56072 -4.03500 1.12613 3 O_3 4.47049
> -1.10357 2.69000 3.46500 1 Pb_2 4.52329
> -1.10357 -2.69000 3.46500 1 Pb_2 4.52329
> -1.10357 2.69000 -3.46500 1 Pb_2 4.52329
> -1.10357 -2.69000 -3.46500 1 Pb_2 4.52329
> 3.12143 2.69000 2.25225 1 Pb_3 4.69596
> 3.12143 -2.69000 2.25225 1 Pb_3 4.69596
> -2.66429 4.03500 -2.33887 3 O_4 5.37122
> -2.66429 -4.03500 -2.33887 3 O_4 5.37122
> 0.00000 5.38000 0.00000 1 Pb_4 5.38000
> 0.00000 -5.38000 0.00000 1 Pb_4 5.38000
> -3.14594 0.00000 -4.45460 2 S_6 5.45348
> -2.66429 1.34500 4.59112 3 O_5 5.47593
> -2.66429 -1.34500 4.59112 3 O_5 5.47593
> 5.30406 0.00000 2.47540 2 S_7 5.85326
> 1.56072 1.34500 -5.80387 3 O_6 6.15872
> 1.56072 -1.34500 -5.80387 3 O_6 6.15872
> 3.12143 2.69000 -4.67775 1 Pb_5 6.23384
> 3.12143 -2.69000 -4.67775 1 Pb_5 6.23384
> 1.07906 5.38000 3.24185 2 S_8 6.37325
> 1.07906 -5.38000 3.24185 2 S_8 6.37325
> -5.32857 2.69000 2.25225 1 Pb_6 6.37984
> -5.32857 -2.69000 2.25225 1 Pb_6 6.37984
> 5.78571 1.34500 -2.33887 3 O_7 6.38387
> 5.78571 -1.34500 -2.33887 3 O_7 6.38387
> 1.07906 5.38000 -3.68815 2 S_9 6.61145
> 1.07906 -5.38000 -3.68815 2 S_9 6.61145
> -2.66429 4.03500 4.59112 3 O_8 6.66769
> -2.66429 -4.03500 4.59112 3 O_8 6.66769
> -3.14594 5.38000 2.47540 2 S_10 6.70589
> -3.14594 -5.38000 2.47540 2 S_10 6.70589
> 6.26736 2.69000 -0.22315 2 S_11 6.82391
> 6.26736 -2.69000 -0.22315 2 S_11 6.82391
> 2.04237 2.69000 5.94040 2 S_12 6.83343
> 2.04237 -2.69000 5.94040 2 S_12 6.83343
> 5.30406 0.00000 -4.45460 2 S_13 6.92651
> 0.00000 0.00000 6.93000 1 Pb_7 6.93000
> 0.00000 0.00000 -6.93000 1 Pb_7 6.93000
> 4.22500 5.38000 -1.21275 1 Pb_8 6.94736
> -4.22500 5.38000 -1.21275 1 Pb_8 6.94736
> 4.22500 -5.38000 -1.21275 1 Pb_8 6.94736
> -4.22500 -5.38000 -1.21275 1 Pb_8 6.94736
> 1.56072 6.72500 1.12613 3 O_9 6.99497
> 1.56072 -6.72500 1.12613 3 O_9 6.99497
> -6.40764 2.69000 -0.98960 2 S_14 7.01949
> -6.40764 -2.69000 -0.98960 2 S_14 7.01949
> 4.22500 0.00000 5.71725 1 Pb_9 7.10898
> -4.22500 0.00000 5.71725 1 Pb_9 7.1089
> END
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20110512/33fa9391/attachment.html>
More information about the Ifeffit
mailing list