A worked example (in text!)

---

 

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.

---

 

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

---

 

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.inp file 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 POTENTIALS list.

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 POTENTIALS list 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: ATOMS list:

    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.inp accordingly.