Re: [Ifeffit] Possible bug in atoms files generation by Artemis

[Matt Newville]

Hi Matthew,

On Tue, 26 Mar 2013, Matthew Marcus wrote:

Just to put my bit in, I believe that the most significant advantage of 
higher FEFF versions for EXAFS analysis is that it results in
more reasonable values for E0 for high-Z elements.  I forget whether the 
issue is high-Z scatterer or absorber.  If you use any of the
common prescriptions for defining E0 with, say, Pt metal in FEFF6l, your fit 
will want large values of enot.  That said, I have not done
a real test by comparing FEFF8 and FEFF6 paths.  Has anyone done that?  It 
would be interesting to know what happens if you simulate a

k^n*chi(k) with one program and fit it with the other.
mam


It's been a very long time since I've tried, but, yes I've made 
such comparisons in the past, as well as comparing Feff6 and 
Feff8 to the same "very good data".


Feff 8 actually has a long history.  Initially, EXAFS was 
noticeably worse with Feff8, but it got better over the years to 
the point where I think it's hard to say that Feff8 is worse 
than Feff6 for EXAFS.  As you say, E0 is better (though still 
needs refinement), as is S02.  Feff8 also appears that it is 
better for heavy elements (perhaps Z > 50, but I'm not sure 
anyone has looked at that carefully).  But: the multi-pole 
self-energy introduced around Feff8.5 or so can make a very 
large improvement for the EXAFS.  Whether this can be made 
generally applicable is a separate question.


Just to echo some of Bruce's frustration and build on that (and, 
speaking only for myself):  Basically, we're stuck with Feff6 
because we do not have access to Feff8.  Last I heard, John and 
Josh were working on this, so that Feff8-for-EXAFS would be made 
freely available.  I haven't seen the code yet, but I'm 
optimistic that it will be released someday.


Once this happens, I'll happily start incorporating this into 
Larch.  I'd very much like to replace the pathfinder (as Bruce 
has done in Perl for Demeter) so that distortions are easier to 
track, and allow the EXAFS calculation for a Path to be done 
automatically inside the fitting loop.  That will be some real 
work (anyone out there interested in helping?), and could take 
awhile, but could actually make a difference for modeling.


I'm pretty sure that getting the multi-pole self-energies more 
universally useful would be a big help, but I think there still 
some unknowns there (basically -- how well do you have to know 
the dielectric response for a general system?) that have to be 
worked out.  Getting 1/epsilon for Cu metal is one thing (a 
first step!), but getting it for As sorbed onto ferrihydrite or 
would be more challenging


--Matt
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] plotting

[Jeff Terry]

Matt is correct. The graphics in Larch are much better than the graphics in the 
old version of ifeffit. 

I may go back to using the command line. 

Jeff


On Mar 26, 2013, at 6:12 PM, Matt Newville  wrote:

> 
> 
> The poor quality of the graphics in the older versions of Ifeffit /
> Horae was always been a disappointment to me.   It's certainly
> reasonable to say that exporting to another program is necessary, but
> I believe the latest versions should and do have much higher quality
> graphics.   Larch certainly has much better graphics than Ifeffit.
> See for example:
>
> http://xraypy.github.com/xraylarch/xafs/xafsft.html#examples-forward-xafs-fourier-transforms
> 
> In the on-line docs, the graphics may look mediocre because they are
> scaled, but if you click on them you will see the PNG file created
> directly by saving the image from the Plot window (or cut with Ctrl-C
> and pasted directly into presentation software).   Another example
> (from the feffit chapter):
> http://xraypy.github.com/xraylarch/_images/feffit_feo_r.png
> 
> shows the Greek characters and mathematical rendering, generated using
> latex notation.   Depending on what you need, these may publication
> quality graphs,and they can be copied directly from the Plotting
> windows into other applications (for example, Ctrl-C to copy to
> clipboard works).   The axis labels (plain text or latex),  colors,
> symbols, line widths, and so on can be adjusted from a Plot
> Configuration window after the plot is drawn, see
>
> http://xraypy.github.com/xraylarch/plotting/index.html#interactive-use-of-the-plot-windows
> 
> There are many things that cannot be done simply with these plots
> (figure-in-figure, complex stacking), but in principle, Larch can be
> used to generate any of the kinds of plots available from the
> matplotlib library, see
>http://matplotlib.org/gallery.html
> 


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] plotting

[Matt Newville]

Hi,

Sorry for coming in late in this conversation.

I won't disagree that Origin or Igor Pro can be used to make lovely
publication-quality graphics -- those are fine choices.

The poor quality of the graphics in the older versions of Ifeffit /
Horae was always been a disappointment to me.   It's certainly
reasonable to say that exporting to another program is necessary, but
I believe the latest versions should and do have much higher quality
graphics.   Larch certainly has much better graphics than Ifeffit.
See for example:

http://xraypy.github.com/xraylarch/xafs/xafsft.html#examples-forward-xafs-fourier-transforms

In the on-line docs, the graphics may look mediocre because they are
scaled, but if you click on them you will see the PNG file created
directly by saving the image from the Plot window (or cut with Ctrl-C
and pasted directly into presentation software).   Another example
(from the feffit chapter):
 http://xraypy.github.com/xraylarch/_images/feffit_feo_r.png

shows the Greek characters and mathematical rendering, generated using
latex notation.   Depending on what you need, these may publication
quality graphs,and they can be copied directly from the Plotting
windows into other applications (for example, Ctrl-C to copy to
clipboard works).   The axis labels (plain text or latex),  colors,
symbols, line widths, and so on can be adjusted from a Plot
Configuration window after the plot is drawn, see

http://xraypy.github.com/xraylarch/plotting/index.html#interactive-use-of-the-plot-windows

There are many things that cannot be done simply with these plots
(figure-in-figure, complex stacking), but in principle, Larch can be
used to generate any of the kinds of plots available from the
matplotlib library, see
http://matplotlib.org/gallery.html

Of course, this does requires some scripting to make plots.   There
are other good, free choices for making high-quality graphics.  As
others have said, investing some time in learning how to make high
quality graphics is worth the effort.  Origin or Igor Pro are very
good  tools, and would be fine choices for learning and not very
expensive.

But please do not use Excel.  It cannot make publication quality graphics.

Cheers,

--Matt
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] plotting

[Jeff Terry]

s using Ifeffit 
>> Subject: Re: [Ifeffit] generating high res figures
>> Message-ID:
>>
>> Content-Type: text/plain; charset="iso-8859-1"
>> 
>> And to do this, use the Artemis Plot dialog box to generate the chart you
>> want (e.g. the data and fit in magnitude R-space), click the "Save Next
>> Plot to File" button at the very bottom of the dialog box, and click the
>> correct plot button at the top (e.g. R). This lets you save the plot as an
>> ASCII file.
>> 
>> -Jason
>> 
>> On Tue, Mar 26, 2013 at 1:25 PM, Scott Calvin 
>> wrote:
>> 
>>> Hi Eva,
>>> 
>>> Demeter is not intended to be used to produce publication-quality figures.
>>> It's best to export the data, fits, etc., and then use a proper graphing
>>> program to generate figures. Even a spreadsheet will do in a pinch,
>>> although most of us use dedicated scientific graphing software.
>>> 
>>> --Scott Calvin
>>> Sarah Lawrence College
>>> 
>>> On Mar 26, 2013, at 1:13 PM, Eva Vanamee  wrote:
>>> 
>>>> Hi,
>>>> 
>>>> I'm in the happy stages of making figures.
>>>> I'd like to know how to change figure legends, make high resolution
>>> figures from a fit, etc.
>>>> 
>>>> For instance:
>>>> I saved the session file. Can I go back to a particular fit to make a
>>> figure or do I need to rerun it?
>>>> Can I change the figure legends? I used sample 1 and I want to give it a
>>> different name
>>>> Can I use special characters (e.g. Greek letters)?
>>>> Can I adjust the resolution for different formats (talk vs. publication)?
>>>> 
>>>> I am running Demeter 0.9.9.9 under XP.
>>>> 
>>>> Thanks in advance for the help!
>>>> 
>>>> - Eva
>>>> 
>>>> 
>>>> ___
>>>> Ifeffit mailing list
>>>> Ifeffit@millenia.cars.aps.anl.gov
>>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>> 
>>> 
>>> ___
>>> Ifeffit mailing list
>>> Ifeffit@millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> -- next part --
>> An HTML attachment was scrubbed...
>> URL: 
>> <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20130326/d1690776/attachment-0001.htm>
>> 
>> --
>> 
>> Message: 4
>> Date: Tue, 26 Mar 2013 13:25:34 -0400
>> From: Christopher Patridge 
>> To: XAFS Analysis using Ifeffit 
>> Subject: Re: [Ifeffit] generating high res figures
>> Message-ID: <5151da0e.9090...@buffalo.edu>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> 
>> Eva,
>> 
>> I don't how flexible would consider exporting the fits you have 
>> completed and using a plotting software (Excel, Origin, Qplot, 
>> sigmaplot, Igor) to generate the number of adjustments you require.
>> 
>> Chris
>> 
>> 
>> Christopher J. Patridge, PhD
>> NRC Post Doctoral Research Associate
>> Naval Research Laboratory
>> Washington, DC 20375
>> Cell: 315-529-0501
>> 
>> On 3/26/2013 1:13 PM, Eva Vanamee wrote:
>>> Hi,
>>> 
>>> I'm in the happy stages of making figures.
>>> I'd like to know how to change figure legends, make high resolution figures 
>>> from a fit, etc.
>>> 
>>> For instance:
>>> I saved the session file. Can I go back to a particular fit to make a 
>>> figure or do I need to rerun it?
>>> Can I change the figure legends? I used sample 1 and I want to give it a 
>>> different name
>>> Can I use special characters (e.g. Greek letters)?
>>> Can I adjust the resolution for different formats (talk vs. publication)?
>>> 
>>> I am running Demeter 0.9.9.9 under XP.
>>> 
>>> Thanks in advance for the help!
>>> 
>>> - Eva
>>> 
>>> 
>>> ___
>>> Ifeffit mailing list
>>> Ifeffit@millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> 
>> 
>> 
>> --
>> 
>> Message: 5
>> Date: Tue, 26 Mar 2013 18:45:19 +
>> From: &quo

Re: [Ifeffit] plotting

[Jason Gaudet]

This list of alternatives is pretty near exhaustive:

http://alternativeto.net/software/originlab/

Although I personally use Origin.


On Tue, Mar 26, 2013 at 5:07 PM, Scott Calvin wrote:

> Hi Eva,
>
> Personally, I'm pretty happy with Pro Fit. It's a commercial product (like
> Origin) but is much cheaper. It's also got the stupidest name imaginable,
> since Google will assume you misspelled "profit." With that in mind the
> website is http://www.quansoft.com . If you're willing to spend more,
> Igor Pro is a good product.
>
> --Scott Calvin
> Sarah Lawrence College
>
> P.S. Disclosure: I have no financial relationship with either software
> producer.
>
> On Mar 26, 2013, at 4:50 PM, Eva Vanamee  wrote:
>
> > Thanks everyone for the helpful comments! I'll go with exporting to
> Origin.
> > A final question. I am now a Mac user, is there a good alternative to
> Origin?
> >
> > Best,
> >
> > - Eva
> >
>
>
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] plotting

[Bare, Simon R]

be used to produce publication-quality figures.
>> It's best to export the data, fits, etc., and then use a proper graphing
>> program to generate figures. Even a spreadsheet will do in a pinch,
>> although most of us use dedicated scientific graphing software.
>> 
>> --Scott Calvin
>> Sarah Lawrence College
>> 
>> On Mar 26, 2013, at 1:13 PM, Eva Vanamee  wrote:
>> 
>>> Hi,
>>> 
>>> I'm in the happy stages of making figures.
>>> I'd like to know how to change figure legends, make high resolution
>> figures from a fit, etc.
>>> 
>>> For instance:
>>> I saved the session file. Can I go back to a particular fit to make a
>> figure or do I need to rerun it?
>>> Can I change the figure legends? I used sample 1 and I want to give it a
>> different name
>>> Can I use special characters (e.g. Greek letters)?
>>> Can I adjust the resolution for different formats (talk vs. publication)?
>>> 
>>> I am running Demeter 0.9.9.9 under XP.
>>> 
>>> Thanks in advance for the help!
>>> 
>>> - Eva
>>> 
>>> 
>>> ___
>>> Ifeffit mailing list
>>> Ifeffit@millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> 
>> 
>> ___
>> Ifeffit mailing list
>> Ifeffit@millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> 
> -- next part --
> An HTML attachment was scrubbed...
> URL: 
> <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20130326/d1690776/attachment-0001.htm>
> 
> --
> 
> Message: 4
> Date: Tue, 26 Mar 2013 13:25:34 -0400
> From: Christopher Patridge 
> To: XAFS Analysis using Ifeffit 
> Subject: Re: [Ifeffit] generating high res figures
> Message-ID: <5151da0e.9090...@buffalo.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Eva,
> 
> I don't how flexible would consider exporting the fits you have 
> completed and using a plotting software (Excel, Origin, Qplot, 
> sigmaplot, Igor) to generate the number of adjustments you require.
> 
> Chris
> 
> 
> Christopher J. Patridge, PhD
> NRC Post Doctoral Research Associate
> Naval Research Laboratory
> Washington, DC 20375
> Cell: 315-529-0501
> 
> On 3/26/2013 1:13 PM, Eva Vanamee wrote:
>> Hi,
>> 
>> I'm in the happy stages of making figures.
>> I'd like to know how to change figure legends, make high resolution figures 
>> from a fit, etc.
>> 
>> For instance:
>> I saved the session file. Can I go back to a particular fit to make a figure 
>> or do I need to rerun it?
>> Can I change the figure legends? I used sample 1 and I want to give it a 
>> different name
>> Can I use special characters (e.g. Greek letters)?
>> Can I adjust the resolution for different formats (talk vs. publication)?
>> 
>> I am running Demeter 0.9.9.9 under XP.
>> 
>> Thanks in advance for the help!
>> 
>> - Eva
>> 
>> 
>> ___
>> Ifeffit mailing list
>> Ifeffit@millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> 
> 
> 
> --
> 
> Message: 5
> Date: Tue, 26 Mar 2013 18:45:19 +
> From: "Ravel, Bruce" 
> To: XAFS Analysis using Ifeffit 
> Subject: Re: [Ifeffit] generating high res figures
> Message-ID:
>   <47ced3cd722c2a439c0d1d1056b213251f32f...@ex10-mb1.bnl.gov>
> Content-Type: text/plain; charset="iso-8859-7"
> 
> 
> As others said, it is not my intention that A&A be used for publication 
> quality plots, although part of the motivation to make Demeter, as compared 
> to the earlier version, was not make prettier plots.  I, in fact, use screen 
> captures of the plot window regularly in presentations and posters.  But I 
> also do as the others advised -- I export the data to ascii column files and 
> make dedicated plots for my publications.
> 
> Even aside from the fact that I chose not to make Demeter into a fully 
> featured scientific plotting tool, it is wise to spend some time thinking 
> hard about your plots for publication.  Figures are part of the story you are 
> telling in your paper.  It is good for you and good for your reader if you 
> spend the time to make beautiful, expressive plots using a highly capable 
&g

Re: [Ifeffit] plotting

[Scott Calvin]

Hi Eva,

Personally, I'm pretty happy with Pro Fit. It's a commercial product (like 
Origin) but is much cheaper. It's also got the stupidest name imaginable, since 
Google will assume you misspelled "profit." With that in mind the website is 
http://www.quansoft.com . If you're willing to spend more, Igor Pro is a good 
product.

--Scott Calvin
Sarah Lawrence College

P.S. Disclosure: I have no financial relationship with either software producer.

On Mar 26, 2013, at 4:50 PM, Eva Vanamee  wrote:

> Thanks everyone for the helpful comments! I'll go with exporting to Origin.
> A final question. I am now a Mac user, is there a good alternative to Origin?
> 
> Best,
> 
> - Eva
> 


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

[Ifeffit] plotting

[Eva Vanamee]

oftware.
>> 
>> --Scott Calvin
>> Sarah Lawrence College
>> 
>> On Mar 26, 2013, at 1:13 PM, Eva Vanamee  wrote:
>> 
>>> Hi,
>>> 
>>> I'm in the happy stages of making figures.
>>> I'd like to know how to change figure legends, make high resolution
>> figures from a fit, etc.
>>> 
>>> For instance:
>>> I saved the session file. Can I go back to a particular fit to make a
>> figure or do I need to rerun it?
>>> Can I change the figure legends? I used sample 1 and I want to give it a
>> different name
>>> Can I use special characters (e.g. Greek letters)?
>>> Can I adjust the resolution for different formats (talk vs. publication)?
>>> 
>>> I am running Demeter 0.9.9.9 under XP.
>>> 
>>> Thanks in advance for the help!
>>> 
>>> - Eva
>>> 
>>> 
>>> ___
>>> Ifeffit mailing list
>>> Ifeffit@millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> 
>> 
>> ___
>> Ifeffit mailing list
>> Ifeffit@millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> 
> -- next part --
> An HTML attachment was scrubbed...
> URL: 
> <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20130326/d1690776/attachment-0001.htm>
> 
> --
> 
> Message: 4
> Date: Tue, 26 Mar 2013 13:25:34 -0400
> From: Christopher Patridge 
> To: XAFS Analysis using Ifeffit 
> Subject: Re: [Ifeffit] generating high res figures
> Message-ID: <5151da0e.9090...@buffalo.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> Eva,
> 
> I don't how flexible would consider exporting the fits you have 
> completed and using a plotting software (Excel, Origin, Qplot, 
> sigmaplot, Igor) to generate the number of adjustments you require.
> 
> Chris
> 
> 
> Christopher J. Patridge, PhD
> NRC Post Doctoral Research Associate
> Naval Research Laboratory
> Washington, DC 20375
> Cell: 315-529-0501
> 
> On 3/26/2013 1:13 PM, Eva Vanamee wrote:
>> Hi,
>> 
>> I'm in the happy stages of making figures.
>> I'd like to know how to change figure legends, make high resolution figures 
>> from a fit, etc.
>> 
>> For instance:
>> I saved the session file. Can I go back to a particular fit to make a figure 
>> or do I need to rerun it?
>> Can I change the figure legends? I used sample 1 and I want to give it a 
>> different name
>> Can I use special characters (e.g. Greek letters)?
>> Can I adjust the resolution for different formats (talk vs. publication)?
>> 
>> I am running Demeter 0.9.9.9 under XP.
>> 
>> Thanks in advance for the help!
>> 
>> - Eva
>> 
>> 
>> ___
>> Ifeffit mailing list
>> Ifeffit@millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> 
> 
> 
> --
> 
> Message: 5
> Date: Tue, 26 Mar 2013 18:45:19 +
> From: "Ravel, Bruce" 
> To: XAFS Analysis using Ifeffit 
> Subject: Re: [Ifeffit] generating high res figures
> Message-ID:
>   <47ced3cd722c2a439c0d1d1056b213251f32f...@ex10-mb1.bnl.gov>
> Content-Type: text/plain; charset="iso-8859-7"
> 
> 
> As others said, it is not my intention that A&A be used for publication 
> quality plots, although part of the motivation to make Demeter, as compared 
> to the earlier version, was not make prettier plots.  I, in fact, use screen 
> captures of the plot window regularly in presentations and posters.  But I 
> also do as the others advised -- I export the data to ascii column files and 
> make dedicated plots for my publications.
> 
> Even aside from the fact that I chose not to make Demeter into a fully 
> featured scientific plotting tool, it is wise to spend some time thinking 
> hard about your plots for publication.  Figures are part of the story you are 
> telling in your paper.  It is good for you and good for your reader if you 
> spend the time to make beautiful, expressive plots using a highly capable 
> plotting tool.
> 
>> Can I change the figure legends? I used sample 1 and I want to give it a 
>> different name
> 
> Yes.  That's easy.  Group menu -> Rename current group.  Or Shift-ctrl-l.  Or 
> double click on the data group in th

Re: [Ifeffit] Possible bug in atoms files generation by Artemis

[Matthew Marcus]

Just to put my bit in, I believe that the most significant advantage of higher 
FEFF versions for EXAFS analysis is that it results in
more reasonable values for E0 for high-Z elements.  I forget whether the issue 
is high-Z scatterer or absorber.  If you use any of the
common prescriptions for defining E0 with, say, Pt metal in FEFF6l, your fit 
will want large values of enot.  That said, I have not done
a real test by comparing FEFF8 and FEFF6 paths.  Has anyone done that?  It 
would be interesting to know what happens if you simulate a
k^n*chi(k) with one program and fit it with the other.
mam

On 3/26/2013 1:10 PM, Ravel, Bruce wrote:


This is more a documentation bug in the sense that I have not written any 
documentation explaining how to use Feff8 with Demeter.  What's more, I have 
not completely tested using Feff8 and there are probably still missing 
features.  I would not expect Feff8 to work completely to your satisfaction at 
this stage.

Even once I get Feff8 support fully implemented, I have no intention of 
distributing a copy of the Feff8 executable with Demeter.  Indeed, I do not 
have the authority to do so.

That said, you need to go to the File menu -> Preferences, the 
Feff->executable.  Change the value of that parameter to the location on your 
computer where the Feff8 executable can be found.  Demeter is not currently smart 
enough to choose a Feff executable according to how you selected to generate the 
feff.inp file.  It is entirely up to you to do  that correctly.

Feff6 input files often work, in some sense, with the Feff8 executable.  Feff8 
input files will not work with the feff6 executable.  That is the issue you are 
reporting as a bug.

In closing, I'll say two things.  (1) Feff8 is not yet fully supported in 
Demeter -- use it at your own peril.  I will eventually get it fully 
implemented, but it is at this time near the top of my list of priorities.  (2) 
You should go back to the mailing list archives and find the last discussion 
about the relative merits of feff6 and feff8 for EXAFS analysis. I was then and 
remain now rather unconvinced that feff8 does anything substantive for you in 
the context of your EXAFS analysis.

B




--

*From:* ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Devender 
[dev...@rpi.edu]
*Sent:* Tuesday, March 26, 2013 3:26 PM
*To:* XAFS Analysis using Ifeffit
*Subject:* [Ifeffit] Possible bug in atoms files generation by Artemis

Hi,

I ran updater for Demeter 0.9.15. I was using Artemis to calculate paths for Bi 
L3 in Bi2Te3. I saw now the option of using both (FEFF 6 and FEFF 8 style) for 
atoms. Previously, I was using only available option of FEFF6 style. When I 
tried to run atoms selecting FEFF 8, it generated atoms files but when I tried 
to run FEFF calculations it produced following errors.

Error#1
" Unknown keyword: "EDGE" at line:
 EDGE  L3"


Error#2
   "Unknown keyword: "exchange" at line:
 exchange"

I worked around first error by replacing

  "EDGE  L3
  S02   1.0 "- which was generated by atoms when FEFF8 style is selected.

with
"HOLE  4   1.0" and deleting Exchange keyword from feff file. After making 
these edits in feff files, I was able to run FEFF without showing any errors. I have 
attached all the files with appropriate name.

--
Devender
Graduate Student, Materials Science and Engineering
Rensselaer Polytechnic Institute, Troy, NY
Website 



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Possible bug in atoms files generation by Artemis

[Ravel, Bruce]

> In closing, I'll say two things.  (1) Feff8 is not yet fully supported in 
> Demeter -- use it at your own peril.  I will
> eventually get it fully implemented, but it is at this time near the top of 
> my list of priorities

*Not*.  It is *not* near the top of my list of priorities.

D'oh!
B

___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Possible bug in atoms files generation by Artemis

[Ravel, Bruce]

This is more a documentation bug in the sense that I have not written any 
documentation explaining how to use Feff8 with Demeter.  What's more, I have 
not completely tested using Feff8 and there are probably still missing 
features.  I would not expect Feff8 to work completely to your satisfaction at 
this stage.

Even once I get Feff8 support fully implemented, I have no intention of 
distributing a copy of the Feff8 executable with Demeter.  Indeed, I do not 
have the authority to do so.

That said, you need to go to the File menu -> Preferences, the 
Feff->executable.  Change the value of that parameter to the location on your 
computer where the Feff8 executable can be found.  Demeter is not currently 
smart enough to choose a Feff executable according to how you selected to 
generate the feff.inp file.  It is entirely up to you to do  that correctly.

Feff6 input files often work, in some sense, with the Feff8 executable.  Feff8 
input files will not work with the feff6 executable.  That is the issue you are 
reporting as a bug.

In closing, I'll say two things.  (1) Feff8 is not yet fully supported in 
Demeter -- use it at your own peril.  I will eventually get it fully 
implemented, but it is at this time near the top of my list of priorities.  (2) 
You should go back to the mailing list archives and find the last discussion 
about the relative merits of feff6 and feff8 for EXAFS analysis. I was then and 
remain now rather unconvinced that feff8 does anything substantive for you in 
the context of your EXAFS analysis.

B


From: ifeffit-boun...@millenia.cars.aps.anl.gov 
[ifeffit-boun...@millenia.cars.aps.anl.gov] on behalf of Devender 
[dev...@rpi.edu]
Sent: Tuesday, March 26, 2013 3:26 PM
To: XAFS Analysis using Ifeffit
Subject: [Ifeffit] Possible bug in atoms files generation by Artemis

Hi,

I ran updater for Demeter 0.9.15. I was using Artemis to calculate paths for Bi 
L3 in Bi2Te3. I saw now the option of using both (FEFF 6 and FEFF 8 style) for 
atoms. Previously, I was using only available option of FEFF6 style. When I 
tried to run atoms selecting FEFF 8, it generated atoms files but when I tried 
to run FEFF calculations it produced following errors.

Error#1
" Unknown keyword: "EDGE" at line:
EDGE  L3"


Error#2
  "Unknown keyword: "exchange" at line:
exchange"

I worked around first error by replacing

 "EDGE  L3
 S02   1.0 "- which was generated by atoms when FEFF8 style is selected.

with
"HOLE  4   1.0" and deleting Exchange keyword from feff file. After making 
these edits in feff files, I was able to run FEFF without showing any errors. I 
have attached all the files with appropriate name.

--
Devender
Graduate Student, Materials Science and Engineering
Rensselaer Polytechnic Institute, Troy, NY
Website

___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

[Ifeffit] Possible bug in atoms files generation by Artemis

[Devender]

Hi,

I ran updater for Demeter 0.9.15. I was using Artemis to calculate paths
for Bi L3 in Bi2Te3. I saw now the option of using both (FEFF 6 and FEFF 8
style) for atoms. Previously, I was using only available option of FEFF6
style. When I tried to run atoms selecting FEFF 8, it generated atoms files
but when I tried to run FEFF calculations it produced following errors.

Error#1
" Unknown keyword: "EDGE" at line:
EDGE  L3"


Error#2
  "Unknown keyword: "exchange" at line:
exchange"

I worked around first error by replacing

 "EDGE  L3
 S02   1.0 "- which was generated by atoms when FEFF8 style is selected.

with
"HOLE  4   1.0" and deleting Exchange keyword from feff file. After
making these edits in feff files, I was able to run FEFF without showing
any errors. I have attached all the files with appropriate name.

-- 
Devender
Graduate Student, Materials Science and Engineering
Rensselaer Polytechnic Institute, Troy, NY
Website 


feff8_user_generated_file_1.inp
Description: Binary data


feff8_user_generated_file_2.inp
Description: Binary data


feff6_auto_generated_file.inp
Description: Binary data


feff8_auto_generated_file.inp
Description: Binary data
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] generating high res figures

[Ravel, Bruce]

As others said, it is not my intention that A&A be used for publication quality 
plots, although part of the motivation to make Demeter, as compared to the 
earlier version, was not make prettier plots.  I, in fact, use screen captures 
of the plot window regularly in presentations and posters.  But I also do as 
the others advised -- I export the data to ascii column files and make 
dedicated plots for my publications.

Even aside from the fact that I chose not to make Demeter into a fully featured 
scientific plotting tool, it is wise to spend some time thinking hard about 
your plots for publication.  Figures are part of the story you are telling in 
your paper.  It is good for you and good for your reader if you spend the time 
to make beautiful, expressive plots using a highly capable plotting tool.

> Can I change the figure legends? I used sample 1 and I want to give it a 
> different name

Yes.  That's easy.  Group menu -> Rename current group.  Or Shift-ctrl-l.  Or 
double click on the data group in the group list.

> Can I use special characters (e.g. Greek letters)?

Not conveniently.  Strictly speaking, if you observe the weird formatting rules 
of the underlying plotting tool, you can do so.  For example, if you you change 
"Sample 1" to "Sample {/Symbol a}" it will be printed in the legend of the plot 
as "Sample α".  But then you will have a weirdly named data group in the group 
list.  (The rest of the Greek characters are made in the same way.  "Sample 
{/Symbol S}" = "Sample Σ" and so on.)

I have never actually thought about how to make it possible to give a group a 
sensible name and have special characters plotted in the legend.  It doesn't 
seem like a high priority, but I could be persuaded.

> Can I adjust the resolution for different formats (talk vs. publication)?

Your best bet by FAR is to export the data as ascii column files and use your 
favorite plotting tool to export into a vector format, such as PDF or SVG.  The 
beauty of vector formats is that they can rescale without loss of quality.

> I am running Demeter 0.9.9.9 under XP.

You might consider upgrading.  There have been a lot of bug fixes and new 
features since then.   One such feature is the ability to export the most 
recent plot as a PNG or PDF file.

B

___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] generating high res figures

[Christopher Patridge]

Eva,

I don't how flexible would consider exporting the fits you have 
completed and using a plotting software (Excel, Origin, Qplot, 
sigmaplot, Igor) to generate the number of adjustments you require.


Chris


Christopher J. Patridge, PhD
NRC Post Doctoral Research Associate
Naval Research Laboratory
Washington, DC 20375
Cell: 315-529-0501

On 3/26/2013 1:13 PM, Eva Vanamee wrote:

Hi,

I'm in the happy stages of making figures.
I'd like to know how to change figure legends, make high resolution figures 
from a fit, etc.

For instance:
I saved the session file. Can I go back to a particular fit to make a figure or 
do I need to rerun it?
Can I change the figure legends? I used sample 1 and I want to give it a 
different name
Can I use special characters (e.g. Greek letters)?
Can I adjust the resolution for different formats (talk vs. publication)?

I am running Demeter 0.9.9.9 under XP.

Thanks in advance for the help!

- Eva


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] generating high res figures

[Jason Gaudet]

And to do this, use the Artemis Plot dialog box to generate the chart you
want (e.g. the data and fit in magnitude R-space), click the "Save Next
Plot to File" button at the very bottom of the dialog box, and click the
correct plot button at the top (e.g. R). This lets you save the plot as an
ASCII file.

-Jason

On Tue, Mar 26, 2013 at 1:25 PM, Scott Calvin wrote:

> Hi Eva,
>
> Demeter is not intended to be used to produce publication-quality figures.
> It's best to export the data, fits, etc., and then use a proper graphing
> program to generate figures. Even a spreadsheet will do in a pinch,
> although most of us use dedicated scientific graphing software.
>
> --Scott Calvin
> Sarah Lawrence College
>
> On Mar 26, 2013, at 1:13 PM, Eva Vanamee  wrote:
>
> > Hi,
> >
> > I'm in the happy stages of making figures.
> > I'd like to know how to change figure legends, make high resolution
> figures from a fit, etc.
> >
> > For instance:
> > I saved the session file. Can I go back to a particular fit to make a
> figure or do I need to rerun it?
> > Can I change the figure legends? I used sample 1 and I want to give it a
> different name
> > Can I use special characters (e.g. Greek letters)?
> > Can I adjust the resolution for different formats (talk vs. publication)?
> >
> > I am running Demeter 0.9.9.9 under XP.
> >
> > Thanks in advance for the help!
> >
> > - Eva
> >
> >
> > ___
> > Ifeffit mailing list
> > Ifeffit@millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] generating high res figures

[Scott Calvin]

Hi Eva,

Demeter is not intended to be used to produce publication-quality figures. It's 
best to export the data, fits, etc., and then use a proper graphing program to 
generate figures. Even a spreadsheet will do in a pinch, although most of us 
use dedicated scientific graphing software.

--Scott Calvin
Sarah Lawrence College

On Mar 26, 2013, at 1:13 PM, Eva Vanamee  wrote:

> Hi,
> 
> I'm in the happy stages of making figures. 
> I'd like to know how to change figure legends, make high resolution figures 
> from a fit, etc.
> 
> For instance:
> I saved the session file. Can I go back to a particular fit to make a figure 
> or do I need to rerun it?
> Can I change the figure legends? I used sample 1 and I want to give it a 
> different name
> Can I use special characters (e.g. Greek letters)?
> Can I adjust the resolution for different formats (talk vs. publication)?
> 
> I am running Demeter 0.9.9.9 under XP. 
> 
> Thanks in advance for the help!
> 
> - Eva
> 
> 
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

[Ifeffit] generating high res figures

[Eva Vanamee]

Hi,

I'm in the happy stages of making figures. 
I'd like to know how to change figure legends, make high resolution figures 
from a fit, etc.

For instance:
I saved the session file. Can I go back to a particular fit to make a figure or 
do I need to rerun it?
Can I change the figure legends? I used sample 1 and I want to give it a 
different name
Can I use special characters (e.g. Greek letters)?
Can I adjust the resolution for different formats (talk vs. publication)?

I am running Demeter 0.9.9.9 under XP. 

Thanks in advance for the help!

- Eva


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit