14.3. A worked example (in text!)¶
14.3.1. The Atoms input file¶
Here is an example of ATOMS in action. The material is lead
titanate, PbTiO3. The crystallographic literature places this
material in the tetragonal space group P 4 M M. Let's suppose tha
the data were taken in fluorescence at the titanium K-edge. Since the
edge energy is around 5 KeV and the sample was very thick, the I0 and self-absorption corrections are expected to be
significant. That titanium is the central atom is indicated by the
keyword core. ATOMS assumes the K-edge of the titanium
was probed because the atomic number of titanium is less than 57 and
the edge was not otherwise chosen with the edge keyword. The I0
chamber was filled with 50% helium and 50% nitrogen by pressure. This
is indicated by the nitrogen keyword. The size of the cluster to
be printed in feff.inp is chosen with the rmax keyword. The
rpath keyword is used to set the value of RMAX in the feff.inp
file, which indicates the length of the longest path to be calculated.
title PbTiO3 10K,a=3.885,c=4.139
space P 4 m m
a=3.885 c=4.139 nitrogen = 0.5
rmax=5.0 rpath=4.2 core=ti
atom
* At x y z tag
Pb 0.0 0.0 0.0
Ti 0.5 0.5 0.5377
O 0.5 0.5 0.1118 axial
O 0.0 0.5 0.6174 planar
Note that CIF files can also be used as the input to ATOMS and will, in many cases, work just fine. The code that reads the CIF files is rather incomplete and a bit buggy, though. Also, DEMETER will refuse to attempt to import data from a CIF file that contains multiple occupancy for a crystallographic site.
- R.J. Nelmes and W.F. Kuhs. The crystal structure of tetragonal PbTiO3 at room temperature and at 700 K. Solid State Communications, 54(8):721 – 723, 1985. doi:10.1016/0038-1098(85)90595-2.
14.3.2. The Feff input file¶
ATOMS produces the output reproduced below. The absorption
and correction calculations are at the top of the file. All the
CONTROL cards are set to 1 and the PRINT cards are set
to 0. This will run all four modules of FEFF and produce
the default output files. Several other useful FEFF cards
are printed but commented out by an asterisk (*). The unique
potential list is constructed in a simple fashion -- the core atom is
potential 0 and each different atomic species has a single
potential. The atom list is printed in the format required by
FEFF. The atom list has two comment columns. The indexed
atomic symbol and radial distance are written by ATOMS for
your use when reading feff.inp and are ignored by
FEFF.
FEFF will run to completion using the input file generated
by ATOMS. It is still likely that the user will want to
edit feff.inp. Several assumptions are made by ATOMS that
might not hold true. The assignment of unique potentials is made by a
simple algorithm and may not adequately reflect the physics of the
problem. The CONTROL cards are such that all four modules of
FEFF will be run. The FEFF user might want to
run the modules separately. Values for other cards have been assumed
and might not be desired. Other cards have been left out entirely.
Always check your feff.inp file to be sure it is just what you
want.
* This feff6 file was generated by Demeter 0.9.13
* Demeter written by and copyright (c) Bruce Ravel, 2006-2012
* --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
* title = PbTiO3 10K,a=3.885,c=4.139
* space = P 4 m m
* a = 3.88500 b = 3.88500 c = 4.13900
* alpha = 90.00000 beta = 90.00000 gamma = 90.00000
* rmax = 5.00000 core = ti
* shift =
* atoms
* # el. x y z tag
* Pb 0.00000 0.00000 0.00000 Pb
* Ti 0.50000 0.50000 0.53770 Ti
* O 0.50000 0.50000 0.11180 axial
* O 0.00000 0.50000 0.61740 planar
* --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
TITLE PbTiO3 10K,a=3.885,c=4.139
HOLE 1 1.0 * FYI: (Ti K edge @ 4966 eV, second number is S0^2)
* mphase,mpath,mfeff,mchi
CONTROL 1 1 1 1
PRINT 1 0 0 0
RMAX 4.2
*NLEG 4
POTENTIALS
* ipot Z tag
0 22 Ti
1 82 Pb
2 22 Ti
3 8 O
ATOMS * this list contains 94 atoms
* x y z ipot tag distance
0.00000 0.00000 0.00000 0 Ti 0.00000
0.00000 0.00000 -1.76280 3 axial.1 1.76280
1.37355 1.37355 0.32988 3 planar.1 1.97031
-1.37355 1.37355 0.32988 3 planar.1 1.97031
1.37355 -1.37355 0.32988 3 planar.1 1.97031
-1.37355 -1.37355 0.32988 3 planar.1 1.97031
0.00000 0.00000 2.37620 3 axial.2 2.37620
2.74711 0.00000 1.91346 1 Pb.1 3.34783
-2.74711 0.00000 1.91346 1 Pb.1 3.34783
0.00000 2.74711 1.91346 1 Pb.1 3.34783
0.00000 -2.74711 1.91346 1 Pb.1 3.34783
2.74711 0.00000 -2.22554 1 Pb.2 3.53548
-2.74711 0.00000 -2.22554 1 Pb.2 3.53548
0.00000 2.74711 -2.22554 1 Pb.2 3.53548
0.00000 -2.74711 -2.22554 1 Pb.2 3.53548
2.74711 2.74711 0.00000 2 Ti.1 3.88500
-2.74711 2.74711 0.00000 2 Ti.1 3.88500
2.74711 -2.74711 0.00000 2 Ti.1 3.88500
-2.74711 -2.74711 0.00000 2 Ti.1 3.88500
0.00000 0.00000 4.13900 2 Ti.2 4.13900
0.00000 0.00000 -4.13900 2 Ti.2 4.13900
2.74711 2.74711 -1.76280 3 axial.3 4.26623
-2.74711 2.74711 -1.76280 3 axial.3 4.26623
2.74711 -2.74711 -1.76280 3 axial.3 4.26623
-2.74711 -2.74711 -1.76280 3 axial.3 4.26623
1.37355 1.37355 -3.80912 3 planar.2 4.27583
-1.37355 1.37355 -3.80912 3 planar.2 4.27583
1.37355 -1.37355 -3.80912 3 planar.2 4.27583
-1.37355 -1.37355 -3.80912 3 planar.2 4.27583
4.12066 1.37355 0.32988 3 planar.3 4.35607
-4.12066 1.37355 0.32988 3 planar.3 4.35607
1.37355 4.12066 0.32988 3 planar.3 4.35607
-1.37355 4.12066 0.32988 3 planar.3 4.35607
4.12066 -1.37355 0.32988 3 planar.3 4.35607
-4.12066 -1.37355 0.32988 3 planar.3 4.35607
1.37355 -4.12066 0.32988 3 planar.3 4.35607
-1.37355 -4.12066 0.32988 3 planar.3 4.35607
2.74711 2.74711 2.37620 3 axial.4 4.55407
-2.74711 2.74711 2.37620 3 axial.4 4.55407
2.74711 -2.74711 2.37620 3 axial.4 4.55407
-2.74711 -2.74711 2.37620 3 axial.4 4.55407
1.37355 1.37355 4.46888 3 planar.4 4.87280
-1.37355 1.37355 4.46888 3 planar.4 4.87280
1.37355 -1.37355 4.46888 3 planar.4 4.87280
-1.37355 -1.37355 4.46888 3 planar.4 4.87280
END
14.3.3. Modifying the Feff input file¶
There are many reasons why you may want to edit the feff.inp before
running FEFF. Here are some examples.
- Change the absorber
Suppose your absorber is a very dilute dopant such that you do not expect, on the average, that another example of the dopant resides anywhere near the absorber. In that case, you would want to leave the atoms list untouched but change the atomic species of the absorber.
In the example above, let's consider that the dilute absorber is Nb. To make it the absorber, we must modify the
feff.inpfile like so:POTENTIALS * ipot Z tag 0 41 Nb 1 82 Pb 2 22 Ti 3 8 O ATOMS * this list contains 94 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Nb 0.00000
Note that the labels (i.e. the instances of the string “Nb”) are for the benefit of the human reader of the file and are also used by DEMETER to provide some information for the user. The essential edit is to change the Z number of the absorber in the
POTENTIALSlist.- Change a scatterer
Again, consider the situation of a Nb dopant in this crystal. With Ti as the absorber, we need to consider the possibility of a Nb atom in the third coordination shell. To do this, we must adit the
POTENTIALSlist to include Nb:POTENTIALS * ipot Z tag 0 22 Ti 1 82 Pb 2 22 Ti 3 8 O 4 41 Nb
We must then replace one or more of the atoms in the third coordination shell with the new unique potential. Here is one example:
2.74711 2.74711 0.00000 4 Nb 3.88500
Again, the “Nb” label is not used by FEFF in any capacity, but is used by DEMETER.
- Add an unique potential
You may choose to consider the possibility that the FEFF calculation might be improved by allowing the axial and planar oxygen atoms to have their own unique potentials. This probably won't make much of a difference in this case, but in the case of an double bonded oxygenyl ligand (as in a uranyl or vanadyl species), it almost certainly will.
First you must add a unique potential
POTENTIALS * ipot Z tag 0 22 Ti 1 82 Pb 2 22 Ti 3 8 axial 4 8 planar
Then you must modify the potential indeces in the to use the new potential index:
ATOMSlist:0.00000 0.00000 -1.76280 4 axial.1 1.76280 1.37355 1.37355 0.32988 3 planar.1 1.97031 -1.37355 1.37355 0.32988 3 planar.1 1.97031 1.37355 -1.37355 0.32988 3 planar.1 1.97031 -1.37355 -1.37355 0.32988 3 planar.1 1.97031 0.00000 0.00000 2.37620 4 axial.2 2.37620
- Modify feff's parameters
- FEFF has lots of options that can be used to control
the calculation of the muffin tin potentials, to alter the
self-energy model, or to enable other features of the
code. ATOMS directly supports few of these additional
features. Should you wish to use them, you must edit the
feff.inpaccordingly.
DEMETER is copyright © 2009-2016 Bruce Ravel – This document is copyright © 2016 Bruce Ravel
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