[Ifeffit] Ifeffit Digest, Vol 137, Issue 36
Shoaib Muhammad
mshoaibce at gmail.com
Tue Jul 15 10:01:22 CDT 2014
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 at millenia.cars.aps.anl.gov
[mailto:ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of
Dien.Li at srs.gov
Sent: Tuesday, July 15, 2014 11:12 PM
To: ifeffit at 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 at millenia.cars.aps.anl.gov
<mailto:ifeffit-request at millenia.cars.aps.anl.gov>
To: ifeffit at millenia.cars.aps.anl.gov
<mailto:ifeffit at millenia.cars.aps.anl.gov> ,
Date: 07/14/2014 07:10 PM
Subject: Ifeffit Digest, Vol 137, Issue 36
Sent by: ifeffit-bounces at millenia.cars.aps.anl.gov
<mailto:ifeffit-bounces at millenia.cars.aps.anl.gov>
_____
Send Ifeffit mailing list submissions to
ifeffit at millenia.cars.aps.anl.gov
<mailto:ifeffit at 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 at millenia.cars.aps.anl.gov
<mailto:ifeffit-request at millenia.cars.aps.anl.gov>
You can reach the person managing the list at
ifeffit-owner at millenia.cars.aps.anl.gov
<mailto:ifeffit-owner at 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 <bravel at bnl.gov <mailto:bravel at bnl.gov> >
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov
<mailto:ifeffit at millenia.cars.aps.anl.gov> >
Subject: Re: [Ifeffit] ATOM and GDS
Message-ID: <53C4599B.4090601 at bnl.gov <mailto:53C4599B.4090601 at bnl.gov> >
Content-Type: text/plain; charset=ISO-8859-1; format=flowed
On 07/14/2014 04:25 PM, Dien.Li at srs.gov <mailto:Dien.Li at 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 at bnl.gov
<mailto:bravel at 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 <abneycw at uchicago.edu <mailto:abneycw at uchicago.edu> >
To: "ifeffit at millenia.cars.aps.anl.gov
<mailto:ifeffit at millenia.cars.aps.anl.gov> "
<ifeffit at millenia.cars.aps.anl.gov
<mailto:ifeffit at millenia.cars.aps.anl.gov> >
Subject: Re: [Ifeffit] ATOM and GDS
Message-ID:
<B4E36C4B6D5E674FB469E2B23AC64D723729B06C at xm-mbx-04-prod.ad.uchicago.edu
<mailto:B4E36C4B6D5E674FB469E2B23AC64D723729B06C at xm-mbx-04-prod.ad.uchicago.
edu> >
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 at srs.gov <mailto:Dien.Li at srs.gov>
To: ifeffit at millenia.cars.aps.anl.gov
<mailto:ifeffit at millenia.cars.aps.anl.gov>
Subject: [Ifeffit] ATOM and GDS
Message-ID:
<OF5F2EDED2.B07C6B62-ON85257D15.006FF11D-85257D15.007036E1 at srs.gov
<mailto:OF5F2EDED2.B07C6B62-ON85257D15.006FF11D-85257D15.007036E1 at 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <
<http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140714/c3a
6fc91/attachment-0001.htm>
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140714/c3a6
fc91/attachment-0001.htm>
------------------------------
Message: 3
Date: Mon, 14 Jul 2014 16:02:12 -0700
From: Jennifer Carter <jwc137 at case.edu <mailto:jwc137 at case.edu> >
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov
<mailto:ifeffit at millenia.cars.aps.anl.gov> >
Subject: Re: [Ifeffit] Macports ifeffit and Demeter Update
Message-ID:
<CAGMGKq4X==AaxG6ymx2BDS+D=t6eyfnAxTU1cCXnjvU=ivcKvw at mail.gmail.com
<mailto:CAGMGKq4X==AaxG6ymx2BDS+D=t6eyfnAxTU1cCXnjvU=ivcKvw at mail.gmail.com>
>
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 at case.edu
<mailto:jwc137 at case.edu> > 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 @0.9.20-2014-06-06_0
>
> ---> demeter-devel @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 at case.edu
<mailto:jennifer.w.carter at case.edu> <jennifer.w.carter at case.edu
<mailto:jennifer.w.carter at case.edu> >*
>
>
> On Mon, Jul 14, 2014 at 3:00 PM, Schima, Frank <frank.schima at nist.gov
<mailto:frank.schima at nist.gov> >
> 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 at case.edu
<mailto:jwc137 at case.edu> > wrote:
>>
>> when I run
>>
>> *sudo port activate demeter-devel @0.9.20pre10_0*
>> ---> Computing dependencies for demeter-devel
>> ---> Activating demeter-devel @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/Plu
gins/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_deme
ter-devel-0.9.20pre10_0_54f3f2fd9281aa66df973ff2918ccf4354f1f896e5b2bc57d680
266a42be52f1-5435/demeter-devel/main.log
>> Warning: Failed to execute portfile from registry for demeter-devel
>> @0.9.20pre10_0
>> ---> Activating demeter-devel @0.9.20pre10_0
>> Error: port activate failed: Image error:
>>
/opt/local/lib/perl5/site_perl/5.16.3/darwin-thread-multi-2level/Demeter/Plu
gins/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 at case.edu <mailto:jennifer.w.carter at case.edu>
<jennifer.w.carter at case.edu <mailto:jennifer.w.carter at case.edu> >*
>>
>>
>> On Mon, Jul 14, 2014 at 2:46 PM, Schima, Frank <frank.schima at nist.gov
<mailto:frank.schima at nist.gov> >
>> 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 @0.9.20pre10_0
>>>
>>>
>>> -Frank
>>>
>>> On Jul 14, 2014, at 3:43 PM, Jennifer Carter <jwc137 at case.edu
<mailto:jwc137 at case.edu> > 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 @0.9.20pre10_0
>>> demeter-devel @0.9.20-2014-06-06_0
>>> ifeffit @1.2.11c_0+gcc48
>>> ifeffit @1.2.13_0+gcc48 (active)
>>> p5.16-ifeffit @1.0.0_0
>>> p5.16-ifeffit @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 at case.edu <mailto:jennifer.w.carter at case.edu>
<jennifer.w.carter at case.edu <mailto:jennifer.w.carter at case.edu> >*
>>>
>>>
>>> On Mon, Jul 14, 2014 at 2:00 PM, Schima, Frank <frank.schima at nist.gov
<mailto:frank.schima at nist.gov> >
>>> 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 @0.9.20pre10_0 (active)
>>>> ifeffit @1.2.13_0+gcc48 (active)
>>>> p5.16-ifeffit @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 at case.edu
<mailto:jwc137 at case.edu> > 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 at case.edu <mailto:jennifer.w.carter at case.edu>
<jennifer.w.carter at case.edu <mailto:jennifer.w.carter at case.edu> >*
>>>>
>>>>
>>>> On Mon, Jul 14, 2014 at 1:04 PM, Schima, Frank <frank.schima at nist.gov
<mailto:frank.schima at nist.gov> >
>>>> 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 @0.9.20pre10_0 (active)
>>>>> ifeffit @1.2.13_0+gcc48 (active)
>>>>> p5.16-ifeffit @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>
https://www.macports.org/install.php>
>>>>>
>>>>> _______________________________________________
>>>>> Ifeffit mailing list
>>>>> Ifeffit at millenia.cars.aps.anl.gov
<mailto:Ifeffit at millenia.cars.aps.anl.gov>
>>>>> <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
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/20140714/bce
6842e/attachment.htm>
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140714/bce6
842e/attachment.htm>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2014-07-14 at 3.58.41 PM.png
Type: image/png
Size: 1015849 bytes
Desc: not available
URL: <
<http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140714/bce
6842e/attachment.png>
http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140714/bce6
842e/attachment.png>
------------------------------
_______________________________________________
Ifeffit mailing list
Ifeffit at millenia.cars.aps.anl.gov <mailto:Ifeffit at millenia.cars.aps.anl.gov>
<http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
End of Ifeffit Digest, Vol 137, Issue 36
****************************************
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140716/7fe8fcf4/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.jpg
Type: image/jpeg
Size: 28111 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140716/7fe8fcf4/attachment.jpg>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Capture.png
Type: image/png
Size: 49198 bytes
Desc: not available
URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20140716/7fe8fcf4/attachment.png>
More information about the Ifeffit
mailing list