New subject: Ifeffit Digest, Vol 137, Issue 36

15 Jul 2014

      Hi, Bruce

With your instruction, we solved the GDS issue. However, for ATOM, I was
screened out to the link you posted. Is there any way to just send me an
ATOM file that has many more atom entry lines, I can use it as a template.
Thanks you so much.

Dien Li, Ph.D.
Environmental Sciences and Biotechnology
Savannah River National Laboratory
Aiken, South Carolina, 29808
Tel: 803-725-7520

From:   ifeffit-request@millenia.cars.aps.anl.gov
To:     ifeffit@millenia.cars.aps.anl.gov,
Date:   07/14/2014 07:10 PM
Subject:        Ifeffit Digest, Vol 137, Issue 36
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Today's Topics:

   1. Re: ATOM and GDS (Bruce Ravel)
   2. Re: ATOM and GDS (Carter Abney)
   3. Re: Macports ifeffit and Demeter Update (Jennifer Carter)

----------------------------------------------------------------------

Message: 1
Date: Mon, 14 Jul 2014 18:28:43 -0400
From: Bruce Ravel 
To: XAFS Analysis using Ifeffit 
Subject: Re: [Ifeffit] ATOM and GDS
Message-ID: <53C4599B.4090601@bnl.gov>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 07/14/2014 04:25 PM, Dien.Li@srs.gov wrote:
...
For the Demeter version I am using, I found that I could just enter 8
atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms
in ATOMS, and define more variables in GDS? and How? Thanks.
The fact that the "add site" button on the atoms page was broken is
among the things on the list of changes for the version I have been
working to get tested and released.

   https://github.com/bruceravel/demeter/blob/master/Changes.org

As for the GDS page, there are several ways of adding a new GDS entry,
described here

   http://bruceravel.github.io/demeter/artug/gds.html

On the path page, in the box which contains the math expression for a
path parameter, try right clicking on GDS parameter.  It'll pop up a
menu that allows you to define a new parameter.

It seems I neglected to put that last thing in the document -- that
needs to be fixed.

B

--
  Bruce Ravel  ------------------------------------ bravel@bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2
  Building 535A
  Upton NY, 11973

  Homepage:    http://xafs.org/BruceRavel
  Software:    https://github.com/bruceravel

------------------------------

Message: 2
Date: Mon, 14 Jul 2014 22:40:12 +0000
From: Carter Abney 
To: "ifeffit@millenia.cars.aps.anl.gov"

Subject: Re: [Ifeffit] ATOM and GDS
Message-ID:

Content-Type: text/plain; charset="us-ascii"

Dr Li,

If I'm understanding the questions properly, there should be some fairly
straightforward fixes.  Simplest first:  in GDS, there should be a button
on the right side that says "Add GDS."  Clicking on it will give you
additional variables (or definitions, restraints, etc.) in GDS. Otherwise,
you could right-click on the numbers to the left of the "type" column.
You'll get options like "insert blank line above (or below) current row."
This is convenient for keeping your variables grouped intelligently while
fitting.  To the best of my knowledge, there is no maximum number of lines
in GDS, though your number of variables should be limited by 2/3 the
number of independent points available from your data.  Additionally,
you're only allowed a maximum of 10 restraints at any time in a fit.

Regarding Atoms, it sounds like you're trying to manually add elements to
the coordination sphere of your absorbing element.  There should be a
button, "add a site" which will allow you to add more than 8 elements.
That said, I've never prepared my scattering pathways in this fashion
(this probably says more about my inexperience than anything else).  Most
of the time, I call Atoms from Artemis, input a cif file, run atoms, run
feff, and have a list of scattering pathways afterwards.  If your system
isn't crystalline, you can run several Feff calculations with different
cif files which have the correct absorbing atom and an appropriate
scattering atom.  (You have to add each of these Feff calculations in
Artemis individually.)  Then, use the generated scattering paths to model
your data.

Also, Atoms allows a person to modify the input file (I believe they're
referred to as "cards") as a text document from within the Atoms program.
So, if I have a model with no cif file, I can run atoms with any other cif
file to generate some sort of card for feff, then I can edit the card
appropriately by copy/pasting the Cartesian coordinates and defining the
appropriate ipot value for each element.  If you have the card already
generated from another cif file, it's fairly straightforward to edit it to
represent your model.

- Carter

Message: 2
Date: Mon, 14 Jul 2014 16:25:40 -0400
From: Dien.Li@srs.gov
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] ATOM and GDS
Message-ID:

Content-Type: text/plain; charset="us-ascii"

HI, Bruce and Matt

For the Demeter version I am using, I found that I could just enter 8
atoms in ATOM, and define 12 variables in GDS. Could I enter more atoms in
ATOMS, and define more variables in GDS? and How? Thanks.

Dien Li, Ph.D.
Environmental Sciences and Biotechnology Savannah River National
Laboratory Aiken, South Carolina, 29808
Tel: 803-725-7520

Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 36

Dien.Li＠srs.gov

Shoaib Muhammad

Bruce Ravel

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