Bruce Ravel | 28 Jul 15:26 2014

Fwd: problems by using Artemis and Demeter


Marika,

I am responding via the Ifeffit mailing list, which is the appropriate
venue for questions about the software.  Please use it.  It is to your
significant benefit to use the mailing list as it exposes you to other
people who may be able to answer your questions.  This is
particularly useful at a time when I am on vacation, as I was for the
last several days.

You did not identify the version of Artemis that you are using,
although your email suggests that you are not using the most current
version.  I simply do not have the resources to provide support for
any but the most recent version of my software.

Your postscript comment is similarly ambiguous in that you did not tell
me what file you were attempting to import nor what actions you took.
See this page of the document:

http://bruceravel.github.io/demeter/artug/startup/main.html#thefilemenu

and, in particular, note the explanation of the "Import" submenu,
which provides a tool for importing project files (.apj) from the very
old version of Artemis.  As I have discussed many times on the mailing
list, .apj file import is spotty, but has imporved over time as people
have reported problems in a way that is clear and actionable.

Cheers,
B

(Continue reading)

Peng Liu | 26 Jul 18:56 2014
Picon
Picon

Can the degeneracy (N) in Artemis be a variable?

Hi all,

When I model a standard, I know the degeneracy through the other data. 
But for spectra of unknown material, I would like to set degeneracy as a 
variable like the amplitude, deltE0, e.g.. However, I can assign a 
letter to N and define it. Do you have any idea how I should do it?

Thanks for your reply,

Peng

--

-- 
Ph.D. Candidate
Earth and Environmental Sciences, CEIT Bldg. Rm. 2026
University of Waterloo        Ph: 519-888-4567 ext. 37232
200 University Avenue West
Waterloo, Ontario  N2L 3G1    Fax:519-746-3882
p26liu@...
huyanyun | 24 Jul 18:35 2014
Picon
Picon

athena working issues on windows 8 and Ubuntu 14.04

Hi All,

I am writing to inquire if Demeter(athena, artemis) works on a 64-bit
windows 8 system. I was trying to install Demeter 0.9.20 (downloaded from
http://bruceravel.github.io/demeter/)on my 64-bit windows 8 laptop. It
seems install well, at least there were no problems coming out during the
installation. However, when I opened Athena, and imported data (an EXAFS
data file end with .dat), there was no graphic window and no data was
imported into Arthena, which stopped me proceeding.

I had similar problems when I tried to install the Updater package
(version 0.9.18.2) after the 0.9.13 Installer package was installed.

Has anyone known if this problem was caused by the
incompatibility between Demeter and Windows 8, or because I didn't install
any supported package? Or how can I resolve this issue?

I also tried to install the source
code of demeter (version 0.9.20) following the instructions on
http://bruceravel.github.io/demeter/pods/installation.pod.html. All
procedures (step 1 to 4 in the section 'BUILD DEMETER AND ITS
DEPENDENCIES') went smoothly on my Ubuntu 14.04. When it was done, I typed
'athena' or 'artemis' in the terminal under the demeter directory and
athena or artemis were launched. But the graphic interface is still PGPLOT,
rather than GNUPLOT, although I have installed GNUPLOT before I built demeter.

Besides that, the data column window opened through 'open files' cannot be
imported, as there is no 'OK' button in the bottom left. Also, the athena
version shown is 0.8.061, rather than 0.9.20 which is the version number of
demeter I built. I was really confused about these working issues, stopping
(Continue reading)

Schima, Frank | 17 Jul 18:02 2014

Demeter OS X plot button colors in Athena

Hi Bruce,


We are seeing an issue in Athena where the plot buttons are not colored correctly. According to section 2.1 of the Athena Users’s Guide, the top row of plot buttons highlighted in the image should be the same color (purple) as the plotting option widgets below them. The 2nd row of plot buttons should be yellowish. However on OS X, all plot buttons appear uncolored. By far the best way to illustrate this is with a screenshot of the Athena UI. I hope the attached image is clear enough to show the issue. 

I am running Demeter version 0.9.20pre10 via Macports demeter-devel on OS X 10.9.4.  

BTW, I am happy to work with you on other OS X issues but I am not actually a demeter user and I don’t have much data myself. But if you send me some data, I can follow steps to try to reproduce issues. 


Cheers!
Frank

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Shaofeng Wang | 17 Jul 09:56 2014
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simulating As K edge XANES using full multi scatering method

Dear all,
 
Does anyone have experience for simulating As K edge XANES using multi-scatering method or some other methods. Please introduce some papers or articles to me.
Any help is appreciated.
 
Regards,
Shaofeng
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Jennifer Carter | 16 Jul 16:17 2014

demeter-devel: Athena autosave hang issue

Installed the newest version of the software for the Mac OS X earlier this week.

v129-22-124-229:~ jwc137$ port installed ifeffit p5.16-ifeffit demeter-devel

The following ports are currently installed:

  demeter-devel <at> 0.9.20pre10_0 (active)

  ifeffit <at> 1.2.11c_0+gcc48

  ifeffit <at> 1.2.13_0+gcc48 (active)

  p5.16-ifeffit <at> 1.0.0_0

  p5.16-ifeffit <at> 2_0 (active)


Now when I try to run athena the software hangs on an autosave file. I am unable to click either button the the pop-up menu to advance the software and I get the "application not responding" error. I searched for an athena.autosave file, as discussed in a previous thread about this issue, but don't find one.


v129-22-124-229:~ jwc137$ find athena.autosave

find: athena.autosave: No such file or directory


Cheers

Jennifer

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Dien.Li | 15 Jul 16:11 2014

Re: 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




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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 <bravel-IGkKxAqZmp0@public.gmane.org>
To: XAFS Analysis using Ifeffit <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Subject: Re: [Ifeffit] ATOM and GDS
Message-ID: <53C4599B.4090601-IGkKxAqZmp0@public.gmane.org>
Content-Type: text/plain; charset=ISO-8859-1; format=flowed

On 07/14/2014 04:25 PM, Dien.Li-/3/1maphar8@public.gmane.org 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-IGkKxAqZmp0@public.gmane.org

 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 <abneycw-t4+EzPmVLfD2fBVCVOL8/A@public.gmane.org>
To: "ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org"
                <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Subject: Re: [Ifeffit] ATOM and GDS
Message-ID:
                <B4E36C4B6D5E674FB469E2B23AC64D723729B06C-SJvkjVeHl0Jr3xoJHmkJRaxXIhPunOuTkCn9CZbayVI@public.gmane.org>
               
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-/3/1maphar8@public.gmane.org
To: ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org
Subject: [Ifeffit] ATOM and GDS
Message-ID:
                <OF5F2EDED2.B07C6B62-ON85257D15.006FF11D-85257D15.007036E1-/3/1maphar8@public.gmane.org>
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
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Message: 3
Date: Mon, 14 Jul 2014 16:02:12 -0700
From: Jennifer Carter <jwc137-oNH6vCZdlc4@public.gmane.org>
To: XAFS Analysis using Ifeffit <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Subject: Re: [Ifeffit] Macports ifeffit and Demeter Update
Message-ID:
                <CAGMGKq4X==AaxG6ymx2BDS+D=t6eyfnAxTU1cCXnjvU=ivcKvw-JsoAwUIsXosN+BqQ9rBEUg@public.gmane.org>
Content-Type: text/plain; charset="utf-8"

So I uninstalled both versions of the demeter-devel and then followed the
original instructions for installing a new version of the software

Now the software is hanging on a non-existing autosave file. The window
pops up, but then I get the rainbow wheel of death and I am unable to click
the don't import button.

Jennifer

[image: Inline image 1]
?




On Mon, Jul 14, 2014 at 3:13 PM, Jennifer Carter <jwc137-oNH6vCZdlc4@public.gmane.org> wrote:

> Frank,
>
> Looks like I have two versions of demeter-devel installed
>
> sudo port -f activate demeter-devel
>
> Password:
>
> --->  The following versions of demeter-devel are currently installed:
>
> --->      demeter-devel <at> 0.9.20-2014-06-06_0
>
> --->      demeter-devel <at> 0.9.20pre10_0
>
> Error: port activate failed: Registry error: Please specify the full
> version as recorded in the port registry.
>
>
> How do I specify a the full version?
>
>
> Thanks
>
> Jennifer
>
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Jennifer L.W. Carter
>
> Assistant Professor
> Department of Materials Science and Engineering
> Case Western Reserve University
>
> *500B White Building*
>
>
>
> *10900 Euclid Ave.Cleveland, OH 44106-4901phone: (216)
> 368-4214email: jennifer.w.carter-oNH6vCZdlc4@public.gmane.org <jennifer.w.carter-oNH6vCZdlc4@public.gmane.org>*
>
>
> On Mon, Jul 14, 2014 at 3:00 PM, Schima, Frank <frank.schima-R3+/ord2DXQ@public.gmane.org>
> wrote:
>
>>  Your setup got munged somehow. You need to do what it says. Namely:
>>
>>  sudo port -f activate demeter-devel
>>
>>
>>  -Frank
>>
>>  On Jul 14, 2014, at 3:55 PM, Jennifer Carter <jwc137-oNH6vCZdlc4@public.gmane.org> wrote:
>>
>>  when I run
>>
>>  *sudo port activate demeter-devel <at> 0.9.20pre10_0*
>> --->  Computing dependencies for demeter-devel
>> --->  Activating demeter-devel <at> 0.9.20pre10_0
>> Error: org.macports.activate for port demeter-devel returned: Image
>> error:
>> /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/Plugins/SpecFileLongLine.pm
>> already exists and does not belong to a registered port.  Unable to
>> activate port demeter-devel. Use 'port -f activate demeter-devel' to force
>> the activation.
>> Please see the log file for port demeter-devel for details:
>>
>> /opt/local/var/macports/logs/_opt_local_var_macports_registry_portfiles_demeter-devel-0.9.20pre10_0_54f3f2fd9281aa66df973ff2918ccf4354f1f896e5b2bc57d680266a42be52f1-5435/demeter-devel/main.log
>> Warning: Failed to execute portfile from registry for demeter-devel
>> <at> 0.9.20pre10_0
>> --->  Activating demeter-devel <at> 0.9.20pre10_0
>> Error: port activate failed: Image error:
>> /opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/Plugins/SpecFileLongLine.pm
>> already exists and does not belong to a registered port.  Unable to
>> activate port demeter-devel. Use 'port -f activate demeter-devel' to force
>> the activation.
>>
>>  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>> Jennifer L.W. Carter
>>
>> Assistant Professor
>> Department of Materials Science and Engineering
>> Case Western Reserve University
>>
>> *500B White Building*
>>
>>
>>
>> *10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214
>> email: jennifer.w.carter-oNH6vCZdlc4@public.gmane.org <jennifer.w.carter-oNH6vCZdlc4@public.gmane.org>*
>>
>>
>> On Mon, Jul 14, 2014 at 2:46 PM, Schima, Frank <frank.schima-R3+/ord2DXQ@public.gmane.org>
>> wrote:
>>
>>> For whatever reason, you do not have any version of demeter-devel
>>> active. You must activate the latest version as follows:
>>>
>>>  sudo port activate demeter-devel <at> 0.9.20pre10_0
>>>
>>>
>>>  -Frank
>>>
>>>  On Jul 14, 2014, at 3:43 PM, Jennifer Carter <jwc137-oNH6vCZdlc4@public.gmane.org> wrote:
>>>
>>>  Frank,
>>>
>>>  This is what I get for the following terminal inputs:
>>>
>>>  *169-231-92-234:~ jwc137$ port installed ifeffit p5.16-ifeffit
>>> demeter-devel*
>>> The following ports are currently installed:
>>>   demeter-devel <at> 0.9.20pre10_0
>>>   demeter-devel <at> 0.9.20-2014-06-06_0
>>>   ifeffit <at> 1.2.11c_0+gcc48
>>>   ifeffit <at> 1.2.13_0+gcc48 (active)
>>>   p5.16-ifeffit <at> 1.0.0_0
>>>   p5.16-ifeffit <at> 2_0 (active)
>>> *169-231-92-234:~ jwc137$ ls -l /opt/local/bin/athena*
>>> ls: /opt/local/bin/athena: No such file or directory
>>> *169-231-92-234:~ jwc137$ ls -l /opt/local/bin/atoms*
>>> ls: /opt/local/bin/atoms: No such file or directory
>>> 169-231-92-234:~ jwc137$
>>>
>>>  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>> Jennifer L.W. Carter
>>>
>>> Assistant Professor
>>> Department of Materials Science and Engineering
>>> Case Western Reserve University
>>>
>>> *500B White Building*
>>>
>>>
>>>
>>> *10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214
>>> email: jennifer.w.carter-oNH6vCZdlc4@public.gmane.org <jennifer.w.carter-oNH6vCZdlc4@public.gmane.org>*
>>>
>>>
>>> On Mon, Jul 14, 2014 at 2:00 PM, Schima, Frank <frank.schima-R3+/ord2DXQ@public.gmane.org>
>>> wrote:
>>>
>>>>  Jennifer,
>>>>
>>>>
>>>>  There is nothing else to do.
>>>>
>>>>  What is the output of the following 3 commands?
>>>>
>>>>  port installed ifeffit p5.16-ifeffit demeter-devel
>>>>  ls -l /opt/local/bin/athena
>>>> ls -l /opt/local/bin/atoms
>>>>
>>>>  Here is the my output (on 2 different computers):
>>>>
>>>>  $ port installed ifeffit p5.16-ifeffit demeter-devel
>>>> The following ports are currently installed:
>>>>   demeter-devel <at> 0.9.20pre10_0 (active)
>>>>   ifeffit <at> 1.2.13_0+gcc48 (active)
>>>>   p5.16-ifeffit <at> 2_0 (active)
>>>>
>>>>  $ ls -l /opt/local/bin/athena
>>>> lrwxr-xr-x  1 root  admin  43 Jul 14 10:53 /opt/local/bin/athena ->
>>>> /opt/local/libexec/perl5.16/sitebin/dathena
>>>>
>>>>  $ ls -l /opt/local/bin/atoms
>>>> lrwxr-xr-x  1 root  admin  45 Jul 14 10:53 /opt/local/bin/atoms ->
>>>> /opt/local/libexec/perl5.16/sitebin/atoms-gui
>>>>
>>>>  As for that perl command, make sure you are using Macports perl.
>>>>
>>>>  $ which perl
>>>> /opt/local/bin/perl
>>>>
>>>>
>>>>  -Frank
>>>>
>>>>  On Jul 14, 2014, at 2:47 PM, Jennifer Carter <jwc137-oNH6vCZdlc4@public.gmane.org> wrote:
>>>>
>>>>  Frank,
>>>>
>>>>  I followed the instructions for updating a current version, but now
>>>> when I type "athena" or "atoms" in the terminal I get the message "command
>>>> not found" am I missing a step?
>>>>
>>>>  running  perl -e 'use Demeter; print $INC{"Demeter.pm"}, $/'
>>>>
>>>>  indicates that nothing was installed.
>>>>
>>>>  Thanks
>>>> Jennifer
>>>>
>>>>  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
>>>> Jennifer L.W. Carter
>>>>
>>>> Assistant Professor
>>>> Department of Materials Science and Engineering
>>>> Case Western Reserve University
>>>>
>>>> *500B White Building*
>>>>
>>>>
>>>>
>>>> *10900 Euclid Ave. Cleveland, OH 44106-4901 phone: (216) 368-4214
>>>> email: jennifer.w.carter-oNH6vCZdlc4@public.gmane.org <jennifer.w.carter-oNH6vCZdlc4@public.gmane.org>*
>>>>
>>>>
>>>> On Mon, Jul 14, 2014 at 1:04 PM, Schima, Frank <frank.schima-R3+/ord2DXQ@public.gmane.org>
>>>> wrote:
>>>>
>>>>> Mac OS X users,
>>>>>
>>>>>
>>>>>  Thanks to help from Bruce Ravel and Matt Newville, I have updated
>>>>> ifeffit and Demeter-devel in Macports to fix a number of problems reported.
>>>>>
>>>>>  To update from your current version type the following:
>>>>>
>>>>>  sudo port selfupdate
>>>>> sudo port upgrade outdated
>>>>>
>>>>>  To install from scratch after installing Macports [1]:
>>>>>
>>>>>  sudo port selfupdate
>>>>> sudo port install demeter-devel
>>>>>
>>>>>  When done, your should see the following ports installed:
>>>>>
>>>>>  $ port installed ifeffit p5.16-ifeffit demeter-devel
>>>>> The following ports are currently installed:
>>>>>   demeter-devel <at> 0.9.20pre10_0 (active)
>>>>>   ifeffit <at> 1.2.13_0+gcc48 (active)
>>>>>   p5.16-ifeffit <at> 2_0 (active)
>>>>>
>>>>>  Please reply to the list (NOT to me directly) about how this works
>>>>> for you.
>>>>>
>>>>>
>>>>>  Cheers!
>>>>> Frank
>>>>>
>>>>>  [1] <https://www.macports.org/install.php>
>>>>>
>>>>> _______________________________________________
>>>>> Ifeffit mailing list
>>>>> Ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org
>>>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>>>>
>>>>
>>
>
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Bruce Ravel | 15 Jul 14:25 2014

Fwd: from Rui Si at SSRF: help needed


Hi Rui,

I am CCing my answer to you and to the Ifeffit Mailing List.  It's
always a good idea to use the mailing list as it greatly increases the
number of eyes that get to look at your question.  If you reply to
this, please do so via the mailing list.

In the PDF file you attached, you asked these two questions:

    (1) Why the second peak (ca. 3 Å) in experimental data is missing in
        the Co3O4 model?

I do not know anything about your sample, so this is a tough question.
Are you certain of its phase purity?  Could there be another form of
cobalt oxide present in the sample?

    (2) Why need to add the “shift vector” suggested by Artemis?
        Actually, no action is required and the software change the Co
        core from 0.125, 0.125, 0.125 to 0.5 0.5 0.5, and keep the shift
        vector as 0 0 0.

The purpose of the shift vector is explained here:

 
http://bruceravel.github.io/demeter/artug/atoms/space.html#multipleoriginsandtheshiftkeyword

In the case of the CIF file you attached, the shift vecotr does not
seem required.  The list of atomic coordinates without the shift
vecotr looks right to me.

B

-------- Original Message --------
Subject: 	from Rui Si at SSRF: help needed
Date: 	Tue, 15 Jul 2014 07:33:31 +0000
From: 	司锐 <sirui@...>
To: 	bravel@... <bravel@...>

Hi Bruce,

Here, I have a question needs your help on the EXAFS fittings.

When I tried to fit the Co3O4 standard (cif and apj file attached),
there was a "shift vector" problem, which has been resulted in the
mismatch between experimental data and theoretic model. Please see the
details in the attachment.

I am not familiar with crystal models, and thus I cannot find the key.
Could you please help me?

Many thanks!

Best,

Rui

----------------------------------------------------------
Dr. Rui Si
Shanghai Institute of Applied Physics, Chinese Academy Sciences
Shanghai Synchrotron Radiation Facility
Address:
239 Zhangheng Rd, Pudong District
Shanghai 201204, China
E-mail: sirui@...
Tel: (86)21-33932079
Cell:(86)13301753969

Attachment (artemis-Co3O4): application/octet-stream, 1108 KiB
Attachment (Co3O4 fitting problem.pdf): application/pdf, 172 KiB
Attachment (Co3O4.cif): application/octet-stream, 6724 bytes
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Rana, Jatinkumar Kantilal | 15 Jul 13:37 2014
Picon

crystallite size determination by EXAFS

Dear all,

 

I have some questions regarding crystallite size determination by EXAFS. I am investigating a system where there is a formation of metallic Cu in the system. I could see the presence of metallic Cu in the sample by XRD and EXAFS. However, high resolution TEM does not show any evidence of metallic Cu, perhaps the crystallite size is much smaller than the resolving power of the microscope and/or these crystallites are highly disordered.

 

Nevertheless, I thought of estimating the size of Cu crystallites by EXAFS. I know at least two approaches described by two prominent members of the mailing list, Scott Calvin and Anatoly Frenkel. The approach by Scott Calvin (http://link.aip.org/link/JAPIAU/v94/i1/p778/s1&Agg=doi) estimates crystallite size based on an assumption that they are spherical in shape. On the other hand, Anatoly Frenkel’s approach estimates both size and shape of crystallites based on the number of neighbors in each coordination shell obtained from EXAFS fit http://pubs.acs.org/doi/abs/10.1021/jp012769j

 

I have questions about the second approach. I would like to know how to calculate the number of neighbors in various coordination shells as a function of cluster size for different shapes ? Conversely, if one knows the number of neighbors in various shells from EXAFS fits, then how to correlate those numbers to clusters of different sizes and shapes as discussed by Anatoly Frenkel.

 

I know my questions are very specific, but I am sure many in the list would have already tried both these approaches and may provide some valuable insights.

 

Many thanks in advance !

 

With best regards,

Jatin

 



Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Prof. Dr. Dr. h.c. mult. Joachim Treusch, stv. Vorsitzende Dr. Beatrix Vierkorn-Rudolph
Geschäftsführung: Prof. Dr. Anke Rita Kaysser-Pyzalla, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
D-14109 Berlin

http://www.helmholtz-berlin.de
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Dien.Li | 14 Jul 22:25 2014

ATOM and GDS

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
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Schima, Frank | 14 Jul 22:04 2014

Macports ifeffit and Demeter Update

Mac OS X users,


Thanks to help from Bruce Ravel and Matt Newville, I have updated ifeffit and Demeter-devel in Macports to fix a number of problems reported. 

To update from your current version type the following:

sudo port selfupdate
sudo port upgrade outdated

To install from scratch after installing Macports [1]:

sudo port selfupdate
sudo port install demeter-devel

When done, your should see the following ports installed:

$ port installed ifeffit p5.16-ifeffit demeter-devel
The following ports are currently installed:
  demeter-devel <at> 0.9.20pre10_0 (active)
  ifeffit <at> 1.2.13_0+gcc48 (active)
  p5.16-ifeffit <at> 2_0 (active)

Please reply to the list (NOT to me directly) about how this works for you. 


Cheers!
Frank

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Gmane