.. Artemis document is copyright 2016 Bruce Ravel and released under The Creative Commons Attribution-ShareAlike License http://creativecommons.org/licenses/by-sa/3.0/ A worked example (in text!) =========================== The Atoms input file ~~~~~~~~~~~~~~~~~~~~ Here is an example of :demeter:`atoms` in action. The material is lead titanate, PbTiO\ :sub:`3`. 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 I\ :sub:`0` and self-absorption corrections are expected to be significant. That titanium is the central atom is indicated by the keyword ``core``. :demeter:`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 I\ :sub:`0` 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 :file:`feff.inp` is chosen with the ``rmax`` keyword. The ``rpath`` keyword is used to set the value of ``RMAX`` in the :file:`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 :demeter:`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:`demeter` will refuse to attempt to import data from a CIF file that contains multiple occupancy for a crystallographic site. .. bibliography:: ../artemis.bib :filter: author % "Nelmes" :list: bullet The Feff input file ~~~~~~~~~~~~~~~~~~~ :demeter:`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 :demeter:`feff` and produce the default output files. Several other useful :demeter:`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 :demeter:`feff`. The atom list has two comment columns. The indexed atomic symbol and radial distance are written by :demeter:`atoms` for your use when reading :file:`feff.inp` and are ignored by :demeter:`feff`. :demeter:`feff` will run to completion using the input file generated by :demeter:`atoms`. It is still likely that the user will want to edit :file:`feff.inp`. Several assumptions are made by :demeter:`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 :demeter:`feff` will be run. The :demeter:`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 :file:`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 :file:`feff.inp` before running :demeter:`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 :file:`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 :quoted:`Nb`) are for the benefit of the human reader of the file and are also used by :demeter:`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 :quoted:`Nb` label is not used by :demeter:`feff` in any capacity, but is used by :demeter:`demeter`. **Add an unique potential** You may choose to consider the possibility that the :demeter:`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** :demeter:`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. :demeter:`atoms` directly supports few of these additional features. Should you wish to use them, you must edit the :file:`feff.inp` accordingly.