[Ifeffit] Atoms & Feff for Ferrihydrite Structure
Bruce Ravel
bravel at bnl.gov
Thu Jan 10 15:15:13 CST 2008
On Thursday 10 January 2008 15:00:19 Voegelin Andreas wrote:
> Using Atoms (latest version of Artemis), I tried to calculate a Feff
> input file based on a recently published structure for 6-Line
> Ferrihydrite (Michel et al, Science, 2007).
>
> Attached: Atoms input file generated with Artemis.
>
> For all three Fe sites as core (Fe1 and Fe2 octahedral, Fe3
> tetrahedral), running Atoms yields Feff files with "overlapping atoms"
> located close to each other. The Artemis error messages after running
> Feff suggests that a shift vector may be needed in order to obtain
> correct Feff input files.
>
> As a "non-crystallographer", I would be grateful for advice on how this
> problem can be solved.
Andreas,
I'm pretty sure I don't count as a crystallographer, and after looking
into this problem, I'm not sure I am confortable calling myself a
programmer either ;-)
This atoms.inp file (which you copied verbatim from the Science
article) triggers a bug I have never seen before in Atoms. When each
unique crystal position is expanded to fill the unit cell, the
symmetries of the cell will, in many cases, generate a particular
position more than once. Atoms has an algorithm which catches those
and throws away the repeats. It attempts to treat numerical precision
correctly in the sense that two positions that differ by a very small
fraction are considered the same. Typically that algorithm handles
the level of numerical precision in cell constants and site
coordinates given in the Science article without a problem (with the
exception of the high symmetry 1/3 and 2/3 positions). In fact, I
have never seen a situation where the algorithm failed as it did here
-- and I have looked at a lot of atoms.inp files over the years.
There is no work-around short of my fixing the algorithm in the next
horae release. The only helpful thing I can think of is to attach
three feff.inp files -- one for each Fe site -- to this message which
I generated with a specially modified version of my demeter code base.
That's not a very gratifying situation for either of us, but it should
get you over the immediate hurdle.
B
--
Bruce Ravel ------------------------------------ bravel at bnl.gov
National Institute of Standards and Technology
Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2
Building 535A
Upton NY, 11973
My homepage: http://xafs.org/BruceRavel
EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
-------------- next part --------------
* This Feff6 input file was generated by Demeter 0.0.1
* Demeter written by and copyright (c) 2006-2007 Bruce Ravel
*-----------------------------------------------------------------
* These crystallographic data were used:
*
* space = 186
* a = 5.92800 b = 5.92800 c = 9.12600
* alpha = 90.00000 beta = 90.00000 gamma = 120.00000
* rmax = 4.00000 core = 4.0
* shift = 0 0 0 # fix me!
* atoms
* el. x y z tag
* Fe 0.16950 0.83040 0.63650 Fe1
* Fe 0.33333 0.66667 0.33790 Fe2
* Fe 0.33333 0.66667 0.95950 Fe3
* O 0.00000 0.00000 0.04460 O1
* O 0.33333 0.66667 0.76340 O2
* O 0.16970 0.83020 0.24670 O3
* O 0.52270 0.47730 0.97960 O4
*
*-----------------------------------------------------------------
* Absorption:
*
* total mu*x=1: 7.335 microns, unit edge step: 8.640 microns
* specific gravity: 4.870
*
* normalization correction: 0.00061 ang^2
* i0 correction: 0.00079 ang^2
* self absorption correction: -0.00040 ang^2
* amplitude factor: 4.416
* net correction: 0.00100 ang^2
*-----------------------------------------------------------------
TITLE 6L-Ferrihydrite
TITLE Michel et al, Science, 2007
HOLE 1 1.0 * FYI: (Fe K edge @ 7112 eV, second number is S0^2)
* mphase,mpath,mfeff,mchi
CONTROL 1 1 1 1
PRINT 1 0 0 0
RMAX 4.0
NLEG 4
*CRITERIA curved plane
POTENTIALS
* ipot Z tag
0 26 Fe
1 26 Fe
2 8 O
ATOMS * this list contains 26 atoms
* x y z ipot tag distance
0.00000 0.00000 0.00000 0 Fe1 0.00000
-0.87069 -1.50749 -0.83868 2 O1 1.93236
0.87223 -1.50779 1.00569 2 O3 2.01137
-1.74190 0.00207 1.00569 2 O3 2.01137
0.84056 1.45654 1.15809 2 O2 2.04186
1.57967 0.17636 -1.43187 2 O4 2.13932
-0.63762 1.45651 -1.43187 2 O4 2.13968
2.52224 1.45681 0.00000 1 Fe1 2.91272
-0.00051 2.91272 0.00000 1 Fe1 2.91272
-2.61156 -1.50719 0.00000 1 Fe1 3.01528
-0.00051 -3.01528 0.00000 1 Fe1 3.01528
0.84056 1.45654 -2.72502 1 Fe2 3.20216
2.55186 -1.50752 -1.61530 1 Fe3 3.37547
-2.58194 1.45648 -1.61530 1 Fe3 3.37594
0.84056 1.45654 2.94770 1 Fe3 3.39367
1.57967 2.73666 -1.43187 2 O4 3.46914
2.55186 -1.50752 1.83798 1 Fe2 3.48751
-2.58194 1.45648 1.83798 1 Fe2 3.48797
3.39139 -0.05276 1.00569 2 O3 3.53775
-1.74241 2.91124 1.00569 2 O3 3.53875
0.00103 0.00178 -3.55731 2 O3 3.55731
1.81274 -0.22734 3.13113 2 O4 3.62515
-1.10377 1.45651 3.13113 2 O4 3.62542
-1.74241 -3.01676 1.00569 2 O3 3.62605
1.57967 -3.19134 -1.43187 2 O4 3.83800
-3.55413 -0.22734 -1.43187 2 O4 3.83846
END
-------------- next part --------------
* This Feff6 input file was generated by Demeter 0.0.1
* Demeter written by and copyright (c) 2006-2007 Bruce Ravel
*-----------------------------------------------------------------
* These crystallographic data were used:
*
* space = 186
* a = 5.92800 b = 5.92800 c = 9.12600
* alpha = 90.00000 beta = 90.00000 gamma = 120.00000
* rmax = 4.00000 core = 4.0
* shift = 0 0 0 # fix me!
* atoms
* el. x y z tag
* Fe 0.16950 0.83040 0.63650 Fe1
* Fe 0.33333 0.66667 0.33790 Fe2
* Fe 0.33333 0.66667 0.95950 Fe3
* O 0.00000 0.00000 0.04460 O1
* O 0.33333 0.66667 0.76340 O2
* O 0.16970 0.83020 0.24670 O3
* O 0.52270 0.47730 0.97960 O4
*
*-----------------------------------------------------------------
* Absorption:
*
* total mu*x=1: 7.335 microns, unit edge step: 8.640 microns
* specific gravity: 4.870
*
* normalization correction: 0.00061 ang^2
* i0 correction: 0.00079 ang^2
* self absorption correction: -0.00040 ang^2
* amplitude factor: 4.416
* net correction: 0.00100 ang^2
*-----------------------------------------------------------------
TITLE 6L-Ferrihydrite
TITLE Michel et al, Science, 2007
HOLE 1 1.0 * FYI: (Fe K edge @ 7112 eV, second number is S0^2)
* mphase,mpath,mfeff,mchi
CONTROL 1 1 1 1
PRINT 1 0 0 0
RMAX 4.0
NLEG 4
*CRITERIA curved plane
POTENTIALS
* ipot Z tag
0 26 Fe
1 26 Fe
2 8 O
ATOMS * this list contains 30 atoms
* x y z ipot tag distance
0.00000 0.00000 0.00000 0 Fe2 0.00000
-0.84004 1.45441 -0.83229 2 O3 1.87448
1.67962 0.00027 -0.83229 2 O3 1.87453
-0.83953 -1.45476 -0.83229 2 O3 1.87453
0.73911 1.28012 1.29315 2 O4 1.96399
-1.47817 -0.00003 1.29315 2 O4 1.96399
0.73911 -1.28018 1.29315 2 O4 1.96403
-0.84107 1.45618 2.72502 1 Fe1 3.20213
1.68168 0.00027 2.72502 1 Fe1 3.20216
-0.84056 -1.45654 2.72502 1 Fe1 3.20216
0.00000 0.00000 -3.45328 1 Fe3 3.45328
0.02962 2.96367 -1.83798 1 Fe1 3.48746
-2.58143 -1.45624 -1.83798 1 Fe1 3.48749
2.55186 -1.50752 -1.83798 1 Fe1 3.48751
-2.58194 1.45648 -1.83798 1 Fe1 3.48797
2.55237 1.50776 -1.83798 1 Fe1 3.48799
0.02962 -2.96433 -1.83798 1 Fe1 3.48802
1.71130 2.96394 -0.67989 2 O2 3.48938
-3.42250 -0.00006 -0.67989 2 O2 3.48938
1.71130 -2.96406 -0.67989 2 O2 3.48948
1.71130 2.96394 1.10972 1 Fe3 3.59791
-3.42250 -0.00006 1.10972 1 Fe3 3.59791
1.71130 -2.96406 1.10972 1 Fe3 3.59801
0.97219 1.68382 -3.26985 2 O4 3.80425
-1.94432 -0.00003 -3.26985 2 O4 3.80425
0.97219 -1.68388 -3.26985 2 O4 3.80427
0.00000 0.00000 3.88311 2 O2 3.88311
-1.71125 2.96397 1.88634 2 O1 3.90791
3.42255 -0.00003 1.88634 2 O1 3.90796
-1.71125 -2.96403 1.88634 2 O1 3.90796
END
-------------- next part --------------
* This Feff6 input file was generated by Demeter 0.0.1
* Demeter written by and copyright (c) 2006-2007 Bruce Ravel
*-----------------------------------------------------------------
* These crystallographic data were used:
*
* space = 186
* a = 5.92800 b = 5.92800 c = 9.12600
* alpha = 90.00000 beta = 90.00000 gamma = 120.00000
* rmax = 4.00000 core = 4.0
* shift = 0 0 0 # fix me!
* atoms
* el. x y z tag
* Fe 0.16950 0.83040 0.63650 Fe1
* Fe 0.33333 0.66667 0.33790 Fe2
* Fe 0.33333 0.66667 0.95950 Fe3
* O 0.00000 0.00000 0.04460 O1
* O 0.33333 0.66667 0.76340 O2
* O 0.16970 0.83020 0.24670 O3
* O 0.52270 0.47730 0.97960 O4
*
*-----------------------------------------------------------------
* Absorption:
*
* total mu*x=1: 7.335 microns, unit edge step: 8.640 microns
* specific gravity: 4.870
*
* normalization correction: 0.00061 ang^2
* i0 correction: 0.00079 ang^2
* self absorption correction: -0.00040 ang^2
* amplitude factor: 4.416
* net correction: 0.00100 ang^2
*-----------------------------------------------------------------
TITLE 6L-Ferrihydrite
TITLE Michel et al, Science, 2007
HOLE 1 1.0 * FYI: (Fe K edge @ 7112 eV, second number is S0^2)
* mphase,mpath,mfeff,mchi
CONTROL 1 1 1 1
PRINT 1 0 0 0
RMAX 4.0
NLEG 4
*CRITERIA curved plane
POTENTIALS
* ipot Z tag
0 26 Fe
1 26 Fe
2 8 O
ATOMS * this list contains 30 atoms
* x y z ipot tag distance
0.00000 0.00000 0.00000 0 Fe3 0.00000
0.00000 0.00000 -1.78961 2 O2 1.78961
1.94432 0.00003 0.18343 2 O4 1.95296
-0.97219 -1.68382 0.18343 2 O4 1.95296
-0.97219 1.68388 0.18343 2 O4 1.95301
0.84004 -1.45441 2.62099 2 O3 3.11296
0.83953 1.45476 2.62099 2 O3 3.11299
-1.67962 -0.00027 2.62099 2 O3 3.11299
-0.02962 -2.96367 1.61530 1 Fe1 3.37542
2.58143 1.45624 1.61530 1 Fe1 3.37544
-2.55186 1.50752 1.61530 1 Fe1 3.37547
2.58194 -1.45648 1.61530 1 Fe1 3.37594
-2.55237 -1.50776 1.61530 1 Fe1 3.37596
-0.02962 2.96433 1.61530 1 Fe1 3.37599
0.84107 -1.45618 -2.94770 1 Fe1 3.39364
0.84056 1.45654 -2.94770 1 Fe1 3.39367
-1.68168 -0.00027 -2.94770 1 Fe1 3.39367
0.00000 0.00000 3.45328 1 Fe2 3.45328
1.71125 -2.96397 0.77662 2 O1 3.50951
-3.42255 0.00003 0.77662 2 O1 3.50956
1.71125 2.96403 0.77662 2 O1 3.50956
-0.03168 -2.96367 -1.94201 2 O3 3.54341
2.58245 1.45446 -1.94201 2 O3 3.54344
-2.55083 1.50930 -1.94201 2 O3 3.54346
2.58297 -1.45470 -1.94201 2 O3 3.54391
-2.55134 -1.50954 -1.94201 2 O3 3.54393
-0.03168 2.96433 -1.94201 2 O3 3.54396
3.42250 0.00006 -1.10972 1 Fe2 3.59791
-1.71130 -2.96394 -1.10972 1 Fe2 3.59791
-1.71130 2.96406 -1.10972 1 Fe2 3.59801
END
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