Hi,
One of the most common inquiries that finds its way into my mailbox is
why the dopants capability in Atoms does not do what the user expects.
Typically, the user expects Atoms to write a magical feff.inp file
that correctly accounts for the dopants in the material such that FEFF
can be run using this magic input file to generate fitting standards
or a XANES calculations for the doped material.
I get this question so often, that I want to post a response to both
the feff and ifeffit mailing lists with an obvious subject line.
Then, in the future, I (or even you!) can just point the curious to
this posting.
----------- O -----------
First off, this topic is covered in the Atoms document
http://leonardo.phys.washington.edu/~ravel/software/exafs/doc/Atoms/Atoms/A…
See section 3.4, Dopants.
I also discuss this issue in Chapter 10 of the lecture notes for my
course on EXAFS Analysis Using FEFF and FEFFIT.
http://leonardo.phys.washington.edu/~ravel/course/notes.pdf
The discussion in this posting applies to the old versions (2.50 and
earlier) of Atoms as well as to the current version.
----------- O -----------
Atoms is, except in extremely contrived situations, not capable of
writing a proper feff.inp file for a doped material. This is not a
programming shortcoming of Atoms, but a number theoretic limitation
imposed by the physical model used by FEFF.
In the feff.inp file, there is a big list of atomic coordinates. The
reason that people like using Atoms is because, without Atoms, it is a
pain in the ass to generate that list. The virtue of Atoms is that it
automates that annoying task for a certain class of matter,
i.e. crystals.
FEFF expects a point in space to be either unoccupied or occupied by a
specific atom. A given point may be occupied neither by a fraction of
an atoms nor by two different kinds of atoms.
Let's use a very simple example -- gold doped into fcc copper. In fcc
copper, there are 12 atoms in the first shell. If the level of doping
was, say, 25%, then Atoms could reasonably use a random number
generator to choose three of the 12 first neighbor sites and replace
them with gold atoms. However, what should Atoms do with the second
shell, which contains 6 atoms? 25% of 6 is 1.5. Feff does not allow
a site to be half occupied by an atomic species, thus Atoms would have
to decide either to over-dope or under-dope the second shell.
This problem only gets worse if the doping fraction is not a rational
(in the number theory sense) fraction, if the material is
non-isotropic, or if the materials has multiple sites that the dopant
might want to go to.
Because Atoms cannot solve this problem correctly except in the most
contrived of situations, I decided that Atoms would not attempt to
solve it in any situation. If you specify dopants in Atoms' input
data, the list in the feff.inp file will be be made as if there are no
dopants.
This leads to two big questions:
1. Why are dopants allowed in Atoms?
2. How do one deal with a doped sample?
The first question is the easy one. Atoms does many things other
besides feff.inp generation. Calculations involving tables of
absorption coefficients and simulations of powder diffraction and
DAFS spectra can use dopant information quite well.
The second question is the tricky one and the answer is somewhat
different for EXAFS as for XANES. The chapter in the PDF file
mentioned at the beginning of this posting discusses one approach to
analyzing EXAFS of doped materials. In this posting
http://cars9.uchicago.edu/feff/feffusers/msg00022.html
Scott Calvin adds his two cents worth. The bottom line for EXAFS
analysis is that most dopant problems require running FEFF many times
to deal with the wide variety of local environments one finds in a
doping problem. One of my papers,
A Combined EXAFS and First Principles Theory Study of
Pb(1-x)Ge(x)Te, B. Ravel, E. Cockayne, M. Newville, and K.M. Rabe,
Phys. Rev. B 60, #21, pp. 14632-14642 (1999).
discusses a very thorough approach to one particular case of a doped
material.
The best approach to simulating a XANES spectrum on a doped material
that I am aware of also involves running FEFF many times. One problem
a colleague of mine asked me about some time ago was the situation of
oxygen vacancies in Au2O3. After some discussion, the solution we
came up with was to use Atoms to generate the feff.inp for the pure
material. My friend then wrote a little computer program that would
read in the feff.inp file, randomly remove oxygen atoms from the list,
write the feff.inp file back out with the missing oxygens, and run
FEFF. He would do this repeatedly, each time replacing a different
set of randomly selected atoms and each time saving the result. This
set of computed spectra was then averaged. New calculations were made
and added to the running average until the result stopped changing.
If I remember, it took about 10 calculations to converge.
This random substitution approach would work just as well for dopants
as for vacancies.
I hope that is helpful.
B
--
Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu
Code 6134, Building 3, Room 222
Naval Research Laboratory phone: (1) 202 767 5947
Washington DC 20375, USA fax: (1) 202 767 1697
NRL Synchrotron Radiation Consortium (NRL-SRC)
Beamlines X11a, X11b, X23b, X24c, U4b
National Synchrotron Light Source
Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi folks,
So, today I tried to actually analyze some data that is long overdue
for some attention. I didn't get much analysis done, but I did find
and fix lots of bugs in Artemis and Athena.
Artemis:
** fixed a bug which precluded using third or fourth cumulants in
fits (that was rather serious!)
** clicking buttons in the plot options section does redisplay
** data gets plotted in R when reading data files, project files, or
feffit.inp files
** fixed a bug which made every item in the "select paths for
fitting" menu fail
** title lines now get correctly restored from project files
** a few internal changes that affect how fits get run and results
get displayed
Athena:
** now using the sort argument to read_data, as was discussed in
some mail earlier today
** disable "save as" menu items for spaces that do not make sense for
the current record
** fixed a bug in how markers get displayed in energy plots
** fixed a few other minor bugs, see CHANGES file for details
New source tarballs are now on my website.
Regards,
B
P.S.
I have been working pretty hard lately on the codes and making lots
of releases. Indeed, this is my fourth tarball announcement during
July! That's the open-source philosophy -- "release early and
often". I don't really expect everyone to update their system
everytime I announce a new tarball. Therefore, I am trying to make
it clear what the major changes are so you can decide if you need to
upgrade.
Athena and Atoms are pretty stable these days -- you probably only
need to upgrade if a change addresses a bug that you have noticed
yourself. Artemis, on the other hand, is changing pretty
dramatically. Each release lately has addressed some serious
usability issues. It may even be useful soon ;-)
--
Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu
Code 6134, Building 3, Room 222
Naval Research Laboratory phone: (1) 202 767 5947
Washington DC 20375, USA fax: (1) 202 767 1697
NRL Synchrotron Radiation Consortium (NRL-SRC)
Beamlines X11a, X11b, X23b, X24c, U4b
National Synchrotron Light Source
Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi folks,
I posted a new source tarball for Artemis on my website. Lots of
improvements this time, including:
** a check to see that all guess parameters are used and that all math
expressions use parameters that have been defined
** rearrangement and improvement (I hope!) of the page for defining
guess, def, and set parameters
** fixed more problems that cropped up after deleting individual feff
paths or entire feff calculations. I know I said I had fixed this
in the last release, but this time I think I mean it!!
** many more features of Artemis can operate on the group of selected
paths, including deletion of paths, exporting path parameter
values, and editing path parameter values
** fixed a problem where, in certain situations, the array containing
the background function refined during a fit was overwritten by
another array. This resulted in messed up plots after doing fits
with background refinements.
** and a bunch of minor things -- see the CHANGES file for details
A windows update will follow soon.
Regards,
B
--
Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu
Code 6134, Building 3, Room 222
Naval Research Laboratory phone: (1) 202 767 5947
Washington DC 20375, USA fax: (1) 202 767 1697
NRL Synchrotron Radiation Consortium (NRL-SRC)
Beamlines X11a, X11b, X23b, X24c, U4b
National Synchrotron Light Source
Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi all,
I just wanted to follow up Matt's announcement of the Windows preview
release yesterday. It includes versions of my programs that have been
updated in the last two weeks. For those of you who are linux, unix,
or OSX users, source code tarballs of the latest versions can be found
on my web site.
For Atoms the big changes are mostly in the parts of the code that
compute absorption cross sections from the McMaster, Elam, or other
tables. Several bugs were fixed, including some severe problems in
the McMaster tables and a bug which resulted in negative
(i.e. unphysical) normalization corrections in some situations.
For Athena the changes are fairly numerous and include bug fixes,
changes to the column selection dialog, changes to the behavior of the
groups list, and a few other things.
For Artemis, I have squashed a lot of bugs which lead to strange
behavior or crashes. Many of the problems had to do with deletion of
feff paths. That is now fixed and should work as expected.
As always, poke at them and let me know what needs fixing.
Special thanks this time to Simon Bare and Paul Fons for very helpful
bug reports.
B
--
Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu
Code 6134, Building 3, Room 222
Naval Research Laboratory phone: (1) 202 767 5947
Washington DC 20375, USA fax: (1) 202 767 1697
NRL Synchrotron Radiation Consortium (NRL-SRC)
Beamlines X11a, X11b, X23b, X24c, U4b
National Synchrotron Light Source
Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi Everyone,
There's a new version of the ifeffit windows installer
available at
http://cars.uchicago.edu/ifeffit/src/iffsetup_jul09.exe
This installer uses ifeffit 1.0072 and includes the latest
versions of atoms, athena, and gifeffit, and now includes
artemis, sixpack, and a few other applications.
The main point of this release is to check the installation
process and the running of all the newly available programs.
I'm expecting that we'll need to make some minor changes to
some of the applications, but I'd like to get a release that
can be stable for several months, so would greatly appreciate
as much testing of these versions as possible.
So, all you Windows users out there, here's your chance to help
out! Please try this installer out, and trying running all the
programs. If any of them don't run or crash immediately,
please let us know.
The installer is now 20Mb, and expands to a directory that uses
about 50Mb. If this is a problem, please let us know: we
could probably split the distribution into separate installers
for different programs.
Thanks,
--Matt
Hey,
Today Matt asked me why I don't make one big tarball with Atoms,
Athen, and Artemis all in it. Apparently a few people have complained
to him about problems upgrading them one at a time.
I think that having one big tarball is a great idea and, in fact, I
have been looking forward to the day when all three would be basically
stable and ready for real work. Atoms and Athena are there. Artemis
should be soon.
I'll probably keep with the separate tarballs thing for my own
convenience for a short while longer, but I suspect that in the next
couple of months I'll start doing one huge tarball.
If anyone has a compelling reason for me *not* to do so, speak up!
B
--
Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu
Code 6134, Building 3, Room 222
Naval Research Laboratory phone: (1) 202 767 5947
Washington DC 20375, USA fax: (1) 202 767 1697
NRL Synchrotron Radiation Consortium (NRL-SRC)
Beamlines X11a, X11b, X23b, X24c, U4b
National Synchrotron Light Source
Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi Folks,
I just uploaded new source tarballs for Atoms and Athena to my web
pages.
For Athena, I corrected two small and somewhat obscure bugs that I
found last week. One had to do with the behaviour of the "fix step"
button and the other with how Cromer-Liberman normalizion parameters
were handled internally.
For Atoms, most of the reason for the new release was to correct
mistakes in the absorption library.
1. The McMaster tables now have a correct entry for the element Re
2. The McMaster tables now corectly handle energy ranges between the
L2 and L3 edges
3. The function that computes the normalization correction has much
more error checking and has a few little bugs corrected. It
should never return a negative normalization correction any more
4. A few small changes to WebAtoms, which also benefits by the items
above.
5. A new item in the TkAtoms File menu -- a submenu labeled "Recent
files". The idea here is that you can easily return to an
atoms.inp file you had been looking at earlier in your TkAtoms
session. As currently implemented it is functional, but behaves
a little oddly. The order of the entries is backwards of what
you may expect (i.e. most recent file is last in the list) and
the list never gets truncated. I got tired of fiddling with it,
so I declared it "functional enough";-)
Check out
http://feff.phys.washington.edu/~ravel/software/exafs/
for the latest.
Next week I hope to build new Windows binaries of all three of my
programs based on Matt's most recent release of Ifeffit, so keep
you eyes on this mailing list for that announcement.
As always, comments, suggestions, feature requests, and bug reports
are very welcome.
Regards,
B
--
Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu
Code 6134, Building 3, Room 222
Naval Research Laboratory phone: (1) 202 767 5947
Washington DC 20375, USA fax: (1) 202 767 1697
NRL Synchrotron Radiation Consortium (NRL-SRC)
Beamlines X11a, X11b, X23b, X24c, U4b
National Synchrotron Light Source
Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi folks,
I received an email from a new user last week praising Francois on his
helpful pages (http://www.univ-mlv.fr/~farges/atomsX/) explaining how
to get Atoms up and running on OSX. Now I have a question for you OSX
gurus on this list.
Can someone write up a web page to supplement this explaining how to
get Ifeffit (and, by extension, Athena and Artemis) up and running on
OSX? Or perhaps this exists, in which case I need the URL so I can
make a link on my web pages.
Eventually, I would like there to be some kind of (Fink-based, I
suppose) installer package for OSX, but for the moment it would be
nice to at least give some guidance to the inspired and dedicated OSX
users.
Thanks,
B
--
Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu
Code 6134, Building 3, Room 222
Naval Research Laboratory phone: (1) 202 767 5947
Washington DC 20375, USA fax: (1) 202 767 1697
NRL Synchrotron Radiation Consortium (NRL-SRC)
Beamlines X11a, X11b, X23b, X24c, U4b
National Synchrotron Light Source
Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi,
I fixed several bugs in Artemis last week and today I posted a new
source code tarball. The changes include:
1. fixed several bugs in displaying and using different FT window
choices
2. fixed some bugs affecting deletion and rereading of feff
calculation.
3. added the ability to turn on and off the "include this path in
fit" button for the set of selected paths (i.e. all the paths
highlighted in orange in the list on the right). I also
reorganized the pull-down menus for including/excluding paths from
the fit.
4. paths included in the fit are listed in black text, paths excluded
from the fit are listed in a different color. also things not
intended for plotting (such as the GSD listing) are printed in
italics. this all gives some visual cues to help use the contents
of the list effectively.
5. fixed (I hope!) a serious problem which manifested itself by
having the data appear as a bizarre starburst-like plot in
k-space. Several people had noticed this already.
These are all pretty significant usability improvements.
Special thanks this week go to Paul Fons for helping me track down
several of these problems.
As always, grab the latest from
http://feff.phys.washington.edu/~ravel/software/exafs/
Regards,
B
--
Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu
Code 6134, Building 3, Room 222
Naval Research Laboratory phone: (1) 202 767 5947
Washington DC 20375, USA fax: (1) 202 767 1697
NRL Synchrotron Radiation Consortium (NRL-SRC)
Beamlines X11a, X11b, X23b, X24c, U4b
National Synchrotron Light Source
Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
Hi,
I fixed the following four problems with artemis reported to me last
week:
1. a really bad bug triggered by using capital letters in parameter
names
2. a strange end-of-line problem when artemis was run on unix using
feffNNNN.dat files made on windows
3. the "View paths.dat" button will look for "paths.dat" or
"path00.dat", i.e. it will find the paths file from feff6 or
feff8
4. several related bugs in how the functional form of the FT windows
were chosen and displayed on the screen
I updated the source tarball and posted it on my web site.
http://feff.phys.washington.edu/~ravel/software/exafs/
Artemis currently has the unfortunate, complimetary problems of
lacking documentation while being a complex and unintuitive program.
The best suggestion I can make for now for learning to use it is to
check out the two project files in the examples/Cu/ directory. They
are the ones with the .apj extensions. If you are a feffit user, you
can import your `feffit.inp' files. If you have never used feffit
before, I would recommend reading Chapters 2 and 4 of the `notes.pdf'
file found on the web page for my "EXAFS Analysis Using FEFF and
FEFFIT" course:
http://leonardo.phys.washington.edu/~ravel/course/
Between that and examining the project files, hopefully Artemis will
make some kind of sense.
Thanks especially to Mark Jensen and Michael DeLeon for their email in
the last few days.
Regards,
B
--
Bruce Ravel ----------------------------------- ravel(a)phys.washington.edu
Naval Research Laboratory, Code 6134 phone: (1) 202 767 5947
Washington DC 20375, USA fax: (1) 202 767 1697
NRL Synchrotron Radiation Consortium (NRL-SRC)
Beamlines X11a, X11b, X23b, X24c, U4b
National Synchrotron Light Source
Brookhaven National Laboratory, Upton, NY 11973
My homepage: http://feff.phys.washington.edu/~ravel
EXAFS software: http://feff.phys.washington.edu/~ravel/software/exafs/
