[Ifeffit] Strange problems with Artemis
Jatinkumar Rana
jatinkumar.rana at helmholtz-berlin.de
Fri Aug 27 02:19:30 CDT 2010
Dear users,
I am facing a strange problem with Artemis and i don't know how to get
rid of it. I hope any expert in the mailing lists would help me solving
this problem.
I have EXAFS data on Fe and Mn K-edge for Arrojadite mineral. Since the
crystal structure of this mineral is not known we did neutron
diffraction to refine the structure. To support the neutron diffraction
results, we planned to do EXAFS on this mineral (Fe and Mn k-edge). We
have around 8 different atomic species (i.e. Na,K,Fe,Mn,Al,Cr,O,P) in
the mineral and some of the sites are fractionally occupied.
Since ATOMS can not handle more than 7 potentials and site occupancy
other than unity i have made following changes :
1) replaced Cr with Al, mainly because Cr is present in a few ppm only
(relative importance).
2) set all site occupancy to 1
Even after doing the above changes, i got following error message when i
run FEFF
**************
Feff 6L.02
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 11 20
11 -3.01973 -0.20361 1.44233
20 -3.54653 -0.05083 0.83053
Run continues...
WARNING: TWO ATOMS VERY CLOSE TOGETHER. CHECK INPUT.
atoms 46 62
46 -0.40014 -0.20361 5.03633
62 0.12666 -0.05083 5.64813
Run continues...
Sodium Potassium Aluminium Chromium Iron Manganese Phosphate Hydrate
Al Cr Fe7.53 H2 K1.21 Mn6 Na3 O50 P12
Kallfa\&s, Christoph
Crystal structure, chemical composition and
thermal behaviour of arrojadite
Calculating potentials and phases...
free atom potential and density for atom type 0
free atom potential and density for atom type 1
free atom potential and density for atom type 2
free atom potential and density for atom type 3
free atom potential and density for atom type 4
free atom potential and density for atom type 5
free atom potential and density for atom type 6
free atom potential and density for atom type 7
overlapped potential and density for unique potential 0
overlapped potential and density for unique potential 1
overlapped potential and density for unique potential 2
overlapped potential and density for unique potential 3
overlapped potential and density for unique potential 4
overlapped potential and density for unique potential 5
overlapped potential and density for unique potential 6
overlapped potential and density for unique potential 7
muffin tin radii and interstitial parameters
phase shifts for unique potential 0
Hard tests failed in fovrg.
Muffin-tin radius may be too large; coordination number too small.
phase shifts for unique potential 1
Hard tests failed in fovrg.
Muffin-tin radius may be too large; coordination number too small.
phase shifts for unique potential 2
Hard tests failed in fovrg.
Muffin-tin radius may be too large; coordination number too small.
phase shifts for unique potential 3
Hard tests failed in fovrg.
Muffin-tin radius may be too large; coordination number too small.
phase shifts for unique potential 4
Hard tests failed in fovrg.
Muffin-tin radius may be too large; coordination number too small.
phase shifts for unique potential 5
Hard tests failed in fovrg.
Muffin-tin radius may be too large; coordination number too small.
phase shifts for unique potential 6
Hard tests failed in fovrg.
Muffin-tin radius may be too large; coordination number too small.
phase shifts for unique potential 7
Hard tests failed in fovrg.
Muffin-tin radius may be too large; coordination number too small.
Preparing plane wave scattering amplitudes...
nncrit in prcrit 9
Searching for paths...
Rmax 7.0000 keep and heap limits 0.0000000 0.0000000
Preparing neighbor table
nfound nheap nheapx nsc r
1000 469 469 3 5.2890
2000 730 730 3 5.7147
3000 907 907 3 5.9455
4000 1040 1040 3 6.1157
5000 1177 1177 3 6.2616
6000 1319 1319 3 6.3835
7000 1412 1413 3 6.4825
8000 1443 1444 3 6.5749
9000 1469 1473 3 6.6585
10000 1432 1474 3 6.7377
11000 1367 1474 3 6.8062
12000 1202 1474 3 6.8680
13000 870 1474 3 6.9289
14000 251 1474 3 6.9856
.
.
.
.
.
..
.
This warning indicates a problem in the Atoms list. For some
reason you have atoms that are separated by than 0.93 Angstroms
(or 1.75 Rydberg).
This may be due to the presence of hydrogen atoms in your feff.inp
file, in which case this is an innocuous warning and may be ignored.
However, this may indicate a problem constructing the Atoms
list. The most common cause of this problem is a mistake in the
crystallographic data used on the Atoms page. You may have
incorrect values for lattice constants or angles or incorrect
values for site coordinates. You may need a shift vector to move
the lattice into its standard setting.
Please be aware that Atoms works with 5 digits of precision.
Thus, if you have a site with a coordinate of 1/3, you should use
either "1/3" or "0.33333" on the Atoms page. Using insufficient
precision, say "0.333" is a common cause of this error message.
Artemis has continued on the possibility that the warning is
caused by hydrogen atoms, but be warned that the feff.inp may
require your attention.
************************************
I have attached both *original.cif file* (with all 8 atomic species and
fractional occupancy) and *modified.cif file* (Cr replaced by Al and all
site occupancy set to 1) with this mail for your perusal.
I hope some experts in the mailing list would suggest me some solutions.
Many more thanks in advance for your valuable time and suggestions....
Best regards,
Rana
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