..
Artemis document is copyright 2016 Bruce Ravel and released under
The Creative Commons Attribution-ShareAlike License
http://creativecommons.org/licenses/by-sa/3.0/
.. role:: guess
.. role:: def
.. role:: set
.. role:: after
.. role:: restrain
Bond valence sums
=================
The concept of a bond in inorganic or crystal chemistry is a bit
ambiguous. In two seminal pair of papers, Brown and Altermatt proposed
this definition :quoted:`All neighboring cation-anion distances are
considered to be bonds although not all of equal strength.` In this
model, each bond between atoms i and j has a number |nd| the bond
valence |nd| s\ :sub:`ij` which is inversely proportional to bond
distance. The bond valence is defined as
s\ :sub:`ij`\ = exp((R\ :sub:`0,ij` - R\ :sub:`ij`)/B),
where R\ :sub:`ij` is the contact distance
and R\ :sub:`0,ij` and B are empirically determined parameters.
.. bibliography:: ../artemis.bib
:filter: author % 'Altermatt'
:list: bullet
They searched through the Inorganic Crystal Structures Database to
determine empirical values for s\ :sub:`ij` for over 150 cation/anion
pairs. Other authors have supplemented this work with additional
anion/cation pairs. Most of these are for common cations, such as
oxygen, nitrogen, or sulfur. Interestingly, B is nearly constant across
all bonds and equal to 0.37. For some anions such as K and U, the value
of B can be as high as about 0.6. R\ :sub:`0,ij` depends on the contact
pair and has been tabulated along with B in a database.
The bond valance sum, then, is the sum of s\ :sub:`ij` over all pairs in
a coordination shell: V= |Sigma| s\ :sub:`ij`. The bond valence sum V should be
equal to the formal valence of the absorber cation. This provides a way
of relating coordination number, bond distance, and formal valence in a
way that is useful and directly applicable to EXAFS analysis.
Computing a bond valence sum from a fit
---------------------------------------
:demeter:`artemis` provides a tool for computing a bond valence sum
from a list of paths included in a fit. A set of paths to be included
in the sum can be marked in a path list. Selecting
:menuselection:`Actions --> Compute bond valence sum` will display this
dialog.
.. _fig-bvs:
.. figure:: ../../_images/bvs.png
:target: ../_images/bvs.png
:align: center
The bond valence sum dialog.
Some care is taken to verify that your selection of paths is sensible.
:demeter:`artemis` will notice if you have marked multiple scattering
paths or have marked paths with absorber/scatterer pairs that are not
in the bond valence database. Although it will proceed with a
calculation, :demeter:`artemis` will warn you if it seems as though
you have included paths that do not seem to be a part of the first
coordination shell.
:demeter:`artemis` also tries to make good guesses about the formal
valences of the absorber and scatterer, althoguh it will often guess
wrongly. It is, therefore, essential that you set the valences
correctly using the choice menus at the top of the bond valence
dialog. It is much more likely that the absorber valence will be
guessed incorrectly.
You will notice that one of the valence options for many absorber
species is :quoted:`9`, an obviously wrong value of valence. The bond
valence database says :quoted:`Bond valence parameters for atoms whose
oxidation state is given as 9 do not have an oxidation state specified
in the original citation. They may apply to a particular, but
unspecified, oxidation state or they may be intended to apply to all
oxidation states.`
In order to make the bond valence summation, the degeneracy of each
path included in the sum must be multiplied by its evaluation of s\
:sub:`ij` (which also uses the evaluation of R=R\ :sub:`0`\ + |Delta| R
as the value of R\ :sub:`ij`). Because path degeneracy might need to
consider quite complicated parameterization of the S\ :sub:`0`\
:sup:`2` path parameter as well as the N path parameter,
:demeter:`artemis` will multiply the evaluations of the N and S\
:sub:`0`\ :sup:`2` path parameters together to use as the evaluation
of degeneracy in the summmation. It is up to you, the user, to supply
a value for the actual amplitude reduction factor, S\ :sub:`0`\
:sup:`2` to be divided out of the summation.
Pressing the :button:`Compute,light` button will make the bond valence
sum, reporting its value in the text box. Any feedback will be written
in the larger text control. For a successful calculation, the values
of R\ :sub:`ij` and B obtained from the database will be
displayed. Any warnings about the path selection will be printed in
the feedback box in bold red text.
Using a bond valance sum as a restraint
---------------------------------------
The bond valence sum can be used a :restrain:`restraint` on a
fit. That is, the relationship between formal valence, coordination
number, and bond distance can be used as prior knowledge guiding the
fit. If the absorber/scatterer pair are in the bond valence database,
values for R\ :sub:`0,ij`, B, and the formal valence of the obsorber
can be defined as set parameters. The bond valence sum is expressed as
a def parameter. Finally, the difference between the bond valence sum
and the formal valence are expressed as a :restrain:`restrain`
parameter. These are shown below for the Fe-O bond in FeO. In FeO the
iron atom is of valence 2+ and the oxygen is 2-.
.. _fig-bvsrestrain:
.. figure:: ../../_images/bvs_restrain.png
:target: ../_images/bvs_restrain.png
:align: center
Defining a group of parameters to make a :restrain:`restraint`
based on a bond valence sum.
When the fit is evaluated, the :restrain:`restrain` parameter will be
added in quadrature to the evaluation of |chi|\ :sup:`2`. This sum
will be minimized in the fit. In a fit to FeO, the coordination number
is fixed to 6, the value known from crystallography. By using this
:restrain:`restraint`, the value of |Delta| R will be encouraged to
assume a value that results in a bond valence sum of 2. By increasing
the value of the scale parameter, the strength of the
:restrain:`restraint` is increased. For a very large value of scale,
|Delta| R will constrained to a value that forces the bond valence sum
to 2. For a very small value of scale, the :restrain:`restraint` will
be weak and |Delta| R will be given more freedom to deviate from a
value that casues a bond valence sum of 2.
This example shows the simplest case of a single scattering path
contributing to the bond valence sum. The math expressions to establish
the :restrain:`restraint` would be more complicated for a more disrodered first
shell, but those math expressions would follow the same pattern as this
example.
Using a bond valance sum as an after parameter
----------------------------------------------
The last :demeter:`artemis` trick related to evaluations of bond
valence sums is to use an `after parameter
<../gds.html#parameter-types>`__ to record the bond valence sum to the
`log file <../logjournal.html>`__. Using the same set of parameters
as in the :restrain:`restraint` example, set the BVS formula instead to an
:after:`after` parameter.
.. _fig-bvsafter:
.. figure:: ../../_images/bvs_after.png
:target: ../_images/bvs_after.png
:align: center
Defining an :after:`after` parameter which reports the evaluated
bond valence sum to the log file.
At the end of the fit, the BVS will be evaluated and reported in the
log file just below the :guess:`guess`, :def:`def`, and :set:`set`
parameters, like so:
::
after parameters:
bvs = 2.04154071 # [6*exp( (rij-(2.139+delr)) / b)]