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

Hi, Dien Li, I have not read the whole thread but usually if we click on "Add a site" in Atoms it can add rows without any problem and then we can fill in the information. Kindly see the screen shot. /Shoaib From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Dien.Li@srs.gov Sent: Tuesday, July 15, 2014 11:12 PM To: ifeffit@millenia.cars.aps.anl.gov Subject: Re: [Ifeffit] Ifeffit Digest, Vol 137, Issue 36 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 mailto:ifeffit-request@millenia.cars.aps.anl.gov To: ifeffit@millenia.cars.aps.anl.gov mailto:ifeffit@millenia.cars.aps.anl.gov , Date: 07/14/2014 07:10 PM Subject: Ifeffit Digest, Vol 137, Issue 36 Sent by: ifeffit-bounces@millenia.cars.aps.anl.gov mailto:ifeffit-bounces@millenia.cars.aps.anl.gov _____ Send Ifeffit mailing list submissions to ifeffit@millenia.cars.aps.anl.gov mailto:ifeffit@millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request@millenia.cars.aps.anl.gov mailto:ifeffit-request@millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner@millenia.cars.aps.anl.gov mailto:ifeffit-owner@millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." 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 mailto:bravel@bnl.gov > To: XAFS Analysis using Ifeffit mailto:ifeffit@millenia.cars.aps.anl.gov > Subject: Re: [Ifeffit] ATOM and GDS Message-ID: <53C4599B.4090601@bnl.gov mailto: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 mailto: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 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 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 mailto: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 http://xafs.org/BruceRavel Software: https://github.com/bruceravel https://github.com/bruceravel ------------------------------ Message: 2 Date: Mon, 14 Jul 2014 22:40:12 +0000 From: Carter Abney mailto:abneycw@uchicago.edu > To: "ifeffit@millenia.cars.aps.anl.gov mailto:ifeffit@millenia.cars.aps.anl.gov " mailto: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 mailto:Dien.Li@srs.gov To: ifeffit@millenia.cars.aps.anl.gov mailto:ifeffit@millenia.cars.aps.anl.gov Subject: [Ifeffit] ATOM and GDS Message-ID: mailto:OF5F2EDED2.B07C6B62-ON85257D15.006FF11D-85257D15.007036E1@srs.gov > 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