Re: [Ifeffit] Bug in Athena?

[Webb, Adam]

>--Matt
>
>PS: I think that means I agree with Anatoly!

Me too!  :-)

I like the side-effect of merging the reference when the spectra are merged. 
However, it is the spectra that I merge rather than the refs. The refs can be 
cleaner for alignment though for samples with small edges. 


Adam


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Re: [Ifeffit] Ifeffit development tools?

[Webb, Adam]

> So low level support for interacting at the "transform/filter/magic"
> level exists.  I suspect, however, that you are not really asking
> about low level support.  I suspect that you are looking for something
> more fleshed out:
> 
>   -- Suppose you were doing some quick-XAS and had 10,000 data files
>  to process.  That kind of problem demands a high level of
>  automation.  You really need some more structure than the
>  low-level hook provided by the swig wrapper.
> 
>   -- Suppose you wanted to use Feff to compute the EXAFS spectrum from
>  the list of atoms resulting from a molecular dynamics
>  calculation.  You'd need a way to loop through the box, find all
>  atom pairs, and figure out how to have Feff run on each pair.
>  Again, swig's hook is at a level that's a bit too low.
> 
> Enabling automation and solving problems like those (as well as small
> one-off chores, as well as GUI-writing, as well as ...) is what I am
> aiming for with Demeter.
> 
> Is Demeter what you are looking for?  Hard to say.  It's written in
> Perl, which might not be your cup of tea.  It's still pretty far from
> done, so it's hard to evaluate.  Most of the design specs that I am
> working towards are inconveniently located in my head (although that
> could be fixed).  I've never had a collaborator that I've worked with
> on the same code base, so I am not in the habit of doing so.  All that
> said, if you are interested in Demeter -- I'd be thrilled to figure
> out how to work together.
> 
> B
> 

Exactly,

The question is how best to utilize the existing software. For trivial 
bits it easier for me to just do something in python. However, for 
larger things like your examples I would be unsure what would be best. 
On the one hand it is possible to use the wrappers but I think it misses 
out on the good functionality that is already present in the whole suite 
of programs.


I think Matt had it bang on. The ideal would be to be able to call the 
functions of ifeffit or Hephaestus etc. For example, to use an external 
program which may be any language.

I also think it is possible but not necessarily easy. I have also been 
rather reluctant to re-code a lot of things. So far I have been 
successful by working around it. I can do something and then move the 
results by hand. This works for small projects but it is limiting. I am 
not certain what the exact answer is but I will give it some serious 
thought. Off the top of my head, some sort of API seems obvious but not 
what form this should take.  (client-server, web, plug-in, )

Out of curiosity. Would demeter be able to 'speak' TDL? Or would TDL 
call demeter? I am uncertain what the status is of things like pyperl or 
inline::python. These were supposed to allow python and perl to talk to 
each other. .Net/Mono is advertised to do such things but I don't know 
if anyone wants to go it that direction.

cheers,

Adam



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Re: [Ifeffit] Ifeffit development tools?

[Webb, Adam]

Greetings,

> I do think an ifeffit-dev list and/or wiki area is a fine
> idea.  I don't know how many others would be interested in
> this, but it might allow for more open development, and keep
> the ifeffit mailing list more for usage questions.  Any
> other opinions on this?
> 

I second the idea. A -dev list would also help avoid confusion. I can 
see that people might get really confused if one set of people are 
talking about some software in development and other people are talking 
about the program that people are using.

> Mauro Rovezzi  wrote:
> 
>> For these reasons I would like to know your point of view
>> on the idea to find a standard in the creation of Ifeffit
>> applications in order to permit the interested community
>> to contribute/share in the programming effort.
>> Practically speaking, if someone would like to implement a
>> new functionality based on the Ifeffit library which
>> directives should follow to integrate the existing
>> applications?
> 

I think that there are several possibilities but I think it would best 
to look at where the codebase is going. The development of tdl and 
demeter look like good solutions. The question is how can other people 
connect into these things.
For example, a plugin like structure might be used. Someone adding a new 
function could for example write a plugin to do something like:
1. ask ifeffit for data and other needed information
2. do some tranform/filter/magic on data
3. return data to ifeffit
Other people could use plugin by calling it from within ifeffit. You can 
do this now with the wrappers but it appears to me that this might be 
easier to do with tdl and/or demeter as these things seem better 
designed to do just that. Perhaps Matt or Bruce would like to comment 
further.

Or people could work more directly with tdl and demeter. In the end I 
think that a modular approach would be best. It could be called the 
XAFS-toolbox or something. ;-)

> 
> Well, now that question (TDL??  Are you nuts??) is a fine
> and fair question, and one I've been asked before and in
> fact ask myself on a regular basis.
> 

I also kind of wondered as I am am normally sceptical of creating a new 
language. However, one advantage of creating a mini language is that you 
can tailor it to the specific application. This way you can get the 
language to 'do what I mean' in a given situation.

Cheers,

Adam


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HASYLAB at DESY
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Re: [Ifeffit] Build intrinsic defect vacancy structure with doping atom.

[Webb, Adam]

Dear Pei-chang Tsai,

Vacancies are done in a similar way to dopants. If you want a vacancy
you remove the atom from the list in the location of the vacancy. You
don't need to change the potentials list. Like with dopants, you will
also have to run multiple runs.

Cheers,
Adam Webb

沛昌 蔡 wrote:
> Dear Prof. ;
>   Thanks for your great informations about build doping atoms,
> and now we consider the real intrinsic defect structure for LiNbO3
> single crystal, as people know about Nb vacancy (means there
> is a hole on Nb atom site) can be exist in this crystal, and our
> question is; The input file is correct or not?
>  
> ps: because we had not see the relation example, maybe you
> can remark the mistake on it and e-mail back.
>  
> Thanks for your time and help!
> Pei-chang Tsai
>  
>  
> 
> ___
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E-mail:  [EMAIL PROTECTED]
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Re: [Ifeffit] Re-check for build lower doping concentration structure in TKAtoms program.

[Webb, Adam]

Dear Pei-chang Tsai,

Scott Calvin discussed this issue on the wiki page
http://cars9.uchicago.edu/ifeffit/Doped as do the other links. It is
rare that you can simply substitute the correct number of atoms into the
structure. The input file will not have the exact desired ratio. The
pages linked previously describe this in some detail so I won't repeat
them here.

The bottom line is that you will need to run feff several times. You
will also have to modify your model to account for the correct level of
dopant.

For such a low concentration, I would suggest method 1 on Scott's page
above. This would mean replacing 1 Li with Zn and then adjusting SO2 to
get the right amount.

Cheers,

Adam Webb


沛昌 蔡 wrote:
> Dear Prof:
>   Thanks for your link informations that about AgBr(1-x)Cl(x=0.1667), but
> in our Zn doped case the concentration x=0.06, following your ratio doping
> rule, the doped Zn atom can't replaced the second layer 7 Li atoms, it
> should stand far away from Nb core atom(~7th layer), and we make
> sure the doped effect can't be ignored, so it's a strict situation, and
> we also can't deny the possibility for Zn atom stand the second layer
> Li atoms, so can you tell us the great experiences that you deal
> with these problem.
>  
> Thanks for helping!
> Pei-chang Tsai
>  
> 
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Re: [Ifeffit] Build lower doping concentration structure in TKAtoms program.

[Webb, Adam]

Dear Pei-chang Tsai,

Using dopants in atoms is something which comes up often. It is a FAQ on
the Ieffit wiki.
http://cars9.uchicago.edu/ifeffit/FAQ/FeffitModeling
and a there is a nice page about doped crystals and alloys
http://cars9.uchicago.edu/ifeffit/Doped?highlight=%28CategoryNotBulkCrystals%29

There is also a previous discussion on this mailing list. Bruce gave a
good summary here.
http://cars9.uchicago.edu/pipermail/ifeffit/2002-July/92.html

The wiki pages http://cars9.uchicago.edu/ifeffit/Ifeffit have answers to
many common questions and even a few uncommon ones. It is often the
first place I go when I start a new problem. :-)

I hope this helps and good luck with your structure.

Adam Webb


沛昌 蔡 wrote:
> Dear Prof:
>   We have some questions about build lower doping concentration 
> structure in TKAtoms program, as following;
> Q1: The TKATOM program can build up doping structure for
>lower doping concentration (below 10%) or not?
> Q2: If it can work, how should we build up the doping site?
> Q3: For lower doping case, how do these doped atoms choose where
>to go in TKATOM program, is it have physical description?
>  
> ps: The attach ppt. file show more detail about our questions.
>  
> Thanks for helping!
> Pei-chang Tsai
>   
> 
> 
>  
> 
> 怎樣減少垃圾信？只要看到垃圾信，立即按下「這是垃圾信」按鈕，*垃圾信剋星* 
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Re: [Ifeffit] Plotting problem

[Webb, Adam]

Hi,

In the edit menu there is a handy tool called "Display Ifeffit buffer". 
This shows you the commands that Athena sends to Ifeffit. In fact it is 
possible to send commands yourself. You just enter it into the entry box 
at the bottom of the window.

In answer to your question. The way that I know is to make a plot and 
see what the commands are. You can directly copy them into a text 
editor, make the changes and paste them back into Athena. All the 
labels, colours etc are there.

Adam

Clement Mbudi wrote:
> Hi there,
> 
> Can somebody tell how to get rid of the " all marked groups" default title 
> when plotting several groups together within Athena environment.
> 
> The " change group label" seems to only work for a single group.
> 
> Similarly, how to change titles of both Y and X axes  within Athena ?
> 
> Thanks.
> 
> 
> Clement
> Edmonton, AB
> 
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