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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@bnl.gov>

To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>

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 <abneycw@uchicago.edu>

To: "ifeffit@millenia.cars.aps.anl.gov"

<ifeffit@millenia.cars.aps.anl.gov>

Subject: Re: [Ifeffit] ATOM and GDS

Message-ID:

<B4E36C4B6D5E674FB469E2B23AC64D723729B06C@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@srs.gov

To: ifeffit@millenia.cars.aps.anl.gov

Subject: [Ifeffit] ATOM and GDS

Message-ID:

<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

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Message: 3

Date: Mon, 14 Jul 2014 16:02:12 -0700

From: Jennifer Carter <jwc137@case.edu>

To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>

Subject: Re: [Ifeffit] Macports ifeffit and Demeter Update

Message-ID:

<CAGMGKq4X==AaxG6ymx2BDS+D=t6eyfnAxTU1cCXnjvU=ivcKvw@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@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@case.edu <jennifer.w.carter@case.edu>*

>

>

> On Mon, Jul 14, 2014 at 3:00 PM, Schima, Frank <frank.schima@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@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/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

>> @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/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@case.edu <jennifer.w.carter@case.edu>*

>>

>>

>> On Mon, Jul 14, 2014 at 2:46 PM, Schima, Frank <frank.schima@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@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@case.edu <jennifer.w.carter@case.edu>*

>>>

>>>

>>> On Mon, Jul 14, 2014 at 2:00 PM, Schima, Frank <frank.schima@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@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@case.edu <jennifer.w.carter@case.edu>*

>>>>

>>>>

>>>> On Mon, Jul 14, 2014 at 1:04 PM, Schima, Frank <frank.schima@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
>

>>>>>

>>>>> _______________________________________________

>>>>> Ifeffit mailing list

>>>>> Ifeffit@millenia.cars.aps.anl.gov

>>>>> 
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

>>>>>

>>>>

>>

>

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