Bruce Ravel | 4 Sep 20:06 2015

Re: Deglitching

On 09/04/2015 01:37 PM, Robert Gordon wrote:
>
> I can confirm something funny is happening here. In 0.9.21, the deglitch
> menu would not display
> points. I upgraded to 0.9.22 today and deglitch now displays points, but
> when I choose a point
> in a test data file (As2O3) and double-click, the energy point removed
> is 11804.228, regardless of where
> I double-click. I reverted back to 0.9.21 and with the same dataset,
> this did not occur. In 0.9.21,
> double-click removed the closest point to where I clicked.
>
> I have win10pro x64 and installed the 64-bit versions of 0.9.21, .22

Can we *please* use the mailing list for these things.  It is helpful to 
the next person who runs into these issues if a discoverable record is 
left behind.

Using the preference tool, can you tell me what the value for 
gnuplot->terminal is?  If it is something other than "wxt", try changing 
it to "wxt".  The interaction with the cursor does not work correctly on 
some terminals.

If that's not the problem, then I am at a loss.  I don't see this 
behavior on any of my computers.

B

--

-- 
  Bruce Ravel  ------------------------------------ bravel@...
(Continue reading)

Matt Newville | 4 Sep 17:30 2015

Re: Deglitching

Hi Martina,

On Sep 3, 2015 12:58 PM, "Martina Ralle" <rallem-k1yIFPgn5XM@public.gmane.org> wrote:

Hi Matt,

 

I have a quick question. When I try to deglitch in Athena it won't let me pick a point for deglitching. No matter where I double click it always chooses 8990.

 

Have others encountered this error? I am running athena on a Windows 7 64 bit machine. The latest (not beta) version.

 


Sorry for the trouble.   I haven't seen (or heard of) that myself, but I'll ask the ifeffit mailing list where maybe someone has a better idea what the trouble could be.

 

-martina

 

Martina Ralle, Ph.D.

Assistant Professor

Department of Molecular and Medical Genetics

Mail Code  L103

OHSU

3181 SW Sam Jackson Pk Rd

Portland, OR 97239

Phone 503 494-3225(o) 503 888-6128(m)

 



 
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Anatoly I Frenkel | 29 Aug 15:59 2015

XAFS short course in BNL on Nov 5-7

Dear subscribers,

 

As a follow up to my previous message, the web page for the XAFS short course at Brookhaven and the application form are live:

 

http://workshops.ps.bnl.gov/?w=XAFS2015

 

Please note the application deadline, September 20.

 

Best regards,

Anatoly

 

Anatoly Frenkel, Ph.D.
Professor and Chair, Department of Physics, Yeshiva University
245 Lexington Avenue, New York, NY 10016
Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc
Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel-OKzqDoqOkpk@public.gmane.org
 
 
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Ganesh Subramanian | 28 Aug 23:03 2015
Picon

Re: Error in Running XANES on FEFF8.4 for Cobalt based cluster

Dear Bruce,

Thanks for the response and sorry for the delay in getting back to you. 

I retried the FEFF simulation using structural information from another article (Randaccio, Lucio, et al. Inorganic chemistry 39.15 (2000): 3403-3413). The structural data from this article seems to be widely used by many others in simulating for optical absorption. But here with FEFF, I still run into the same issue of "ATOMS VERY CLOSE TOGETHER" and a couple of other issues. With two different articles suggesting smaller bond distances for a few of their atoms, it seems like the distances are what they are.

I have attached the log files and input file for this trial run. 

Is there any way to circumvent this error without altering the structure ?  

Thanks,

Ganesh
 
From: Bruce Ravel <bravel-IGkKxAqZmp0@public.gmane.org>
To: XAFS Analysis using Ifeffit <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt
        based cluster
Message-ID: <55BA3978.4080801 <at> bnl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 07/29/2015 06:01 PM, Ganesh Subramanian wrote:
> 1. *Using the FOLP card*: The actual cluster size is about 180 atoms
> extending upto 18 A in radial distance from the central cobalt atom. But
> there are quite a few instances of Hydrogen atoms that are too close. I
> tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to
> get a syntax type error, that i cant figure out. I checked the crystal
> structure and the smallest hydrogen bond distance is 0.89 A. (I have
> attached the corresponding input and log file with suffix 'full cluster')

In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you
when you have atoms that are separated by 1.75 Angstroms or less.  That
message has nothing to do with the FOLP setting.

> 2. *SCF for small cluster*: Since the problem with the hydrogen
> distances persisted, I decided to run the calculation for a smaller
> cluster (about 50 atoms). I used the conditions as prescribed for small
> clusters - SCF 5.0 1, FMS 5.0 1, RPATH -1. Those hydrogens that were too
> close (within this smaller cluster, there were about 3 of them, and none
> in the first or second shell of co-ordination) were removed manually.
> Now, I did not have the error on distances, did not require the FOLP
> card to be manually altered, but the log1 file seems to suggest that the
> SCF is not calculated. I cant figure why that is the case. (I have
> attached the corresponding input and log file with suffix 'small cluster')

When I ran feff 8.40, I got same the contents of the log1.dat file, but
with these additional lines:

                 Core-valence separation
   WARNING: fatal error in subroutine corval. Try
     to reduce ca1 in SCF card. If does not help,
   SEND bug report to AUTHORS
   CORVAL-1

I don't quite know what that means, but it gives some hints.  The source
code corval.f tells us that is "Finds the core-valence separation for
the cluster of atoms."  I simply am not knowledgeable enough about the
details of Feff to know why your cluster triggered this warning.

B



--
  Bruce Ravel  ------------------------------------ bravel-IGkKxAqZmp0@public.gmane.org

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 535A
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/


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

Message: 3
Date: Thu, 30 Jul 2015 10:51:30 -0400
From: Bruce Ravel <bravel-IGkKxAqZmp0@public.gmane.org>
To: XAFS Analysis using Ifeffit <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Subject: Re: [Ifeffit] Error in Running XANES on FEFF8.4 for Cobalt
        based cluster
Message-ID: <55BA39F2.4090609 <at> bnl.gov>
Content-Type: text/plain; charset=windows-1252; format=flowed

On 07/30/2015 10:49 AM, Bruce Ravel wrote:
>> 1. *Using the FOLP card*: The actual cluster size is about 180 atoms
>> extending upto 18 A in radial distance from the central cobalt atom. But
>> there are quite a few instances of Hydrogen atoms that are too close. I
>> tried the FOLP with the recommendation for Hydrogen of 0.8, I seem to
>> get a syntax type error, that i cant figure out. I checked the crystal
>> structure and the smallest hydrogen bond distance is 0.89 A. (I have
>> attached the corresponding input and log file with suffix 'full cluster')
>
> In Feff the "TWO ATOMS VERY CLOSE TOGETHER" message gets shouted at you
> when you have atoms that are separated by 1.75 Angstroms or less.  That
> message has nothing to do with the FOLP setting.

Oops!  That message is triggered for atoms separated by 1.75 bohr, which
is about 0.92 Angstrom.

B


--
  Bruce Ravel  ------------------------------------ bravel-IGkKxAqZmp0@public.gmane.org

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 535A
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/


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

Message: 4
Date: Thu, 30 Jul 2015 15:58:12 +0000
From: "Fowler, Joseph W." <joe.fowler-R3+/ord2DXQ@public.gmane.org>
To: "ifeffit <at> millenia.cars.aps.anl.gov"
        <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8)
Message-ID: <D1759C33-50D0-46D4-84D0-4D649CA779A8-R3+/ord2DXQ@public.gmane.org>
Content-Type: text/plain; charset="windows-1252"

Dear Ie-Rang,

I?m the demeter maintainer on MacPorts, but I admit I am anything but a MacPorts guru.

I notice that the error you showed is a failure to install gcc49. I don?t know if that new GCC is compatible with your old version of OS X, but that?s an issue that?s beyond my expertise. You might edit your variants file (it?s /opt/local/etc/macports/variants.conf on my installation) to insist on an earlier version by adding a line containing, e.g., ?+gcc47? or whatever is your installed and preferred version of GCC.

In fact, the port demeter does not depend (directly) on gcc, which you can see by issuing the command

> port echo depof:demeter
> port echo depof:demeter-devel

So it looks to me like you have several steps to get ready for installing demeter.

I admit that I recently discovered?but have not fixed?a flaw in the demeter port description file. The code depends on ports p5.16-file-which and p5.16-math-round, but these are not made explicit. I need to figure out how to add these to the explicit dependency list. I?m just back from vacation and a conference, so I have no excuses now. If you get far enough that you can install *but not run* demeter?s executables, then a workaround for this is

> sudo port install p5.16-file-which p5.16-math-round

And for MacPorts users in general: I understand that the project as a whole is in the process of trying to move to Perl 5.22 instead of 5.16. I?ll be updating the port file to reflect that change, too.

Joe Fowler
NIST Boulder Laboratories


On Jul 29, 2015, at 4:01 PM, ifeffit-request-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org<mailto:ifeffit-request <at> millenia.cars.aps.anl.gov> wrote:

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Today's Topics:

  1. HELP: failed to install gcc49 on mac (v10.6.8) (Ie-Rang Jeon)
  2. Re: HELP: failed to install gcc49 on mac (v10.6.8) (Bruce Ravel)
  3. Error in Running XANES on FEFF8.4 for Cobalt based cluster
     (Ganesh Subramanian)

From: Ie-Rang Jeon <jeon <at> northwestern.edu>
Subject: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8)
Date: July 29, 2015 at 1:11:08 PM MDT
To: "ifeffit <at> millenia.cars.aps.anl.gov" <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Reply-To: XAFS Analysis using Ifeffit <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>


Hello,

I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got.
Could you please help me to figure out what the problem is?

Thank you.
Ie-Rang


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

--->  Building gcc49
Error: org.macports.build for port gcc49 returned: command execution failed
Error: Failed to install gcc49
Please see the log file for port gcc49 for details:
   /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log
Error: The following dependencies were not installed:
.
.
.
Error: Processing of port demeter-devel failed






From: Bruce Ravel <bravel-IGkKxAqZmp0@public.gmane.org>
Subject: Re: [Ifeffit] HELP: failed to install gcc49 on mac (v10.6.8)
Date: July 29, 2015 at 1:21:06 PM MDT
To: XAFS Analysis using Ifeffit <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>
Reply-To: XAFS Analysis using Ifeffit <ifeffit-yJARRRr6MatTopXEvdbuMochTzHAynqa8htcxDm17Xw@public.gmane.org>


On 07/29/2015 03:11 PM, Ie-Rang Jeon wrote:
Hello,

I'm trying to install MacPorts package on my mac (v.10.6.8), and I can't do this. Below are error messages that I got.
Could you please help me to figure out what the problem is?

Thank you.
Ie-Rang

Perhaps there's anything useful in that log file?
B




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

--->  Building gcc49
Error: org.macports.build for port gcc49 returned: command execution failed
Error: Failed to install gcc49
Please see the log file for port gcc49 for details:
    /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc49/gcc49/main.log
Error: The following dependencies were not installed:
.
.
.
Error: Processing of port demeter-devel failed


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--
Bruce Ravel  ------------------------------------ bravel-IGkKxAqZmp0@public.gmane.org

National Institute of Standards and Technology
Synchrotron Science Group at NSLS-II
Building 535A
Upton NY, 11973

Homepage:    http://bruceravel.github.io/home/
Software:    https://github.com/bruceravel
Demeter:     http://bruceravel.github.io/demeter/



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End of Ifeffit Digest, Vol 149, Issue 27
****************************************

 Feff 8.40
  XANES:
 FOLP:
 Expert option, please read documentation carefully and check your results.
 MeCbl-Groundstate-Kedge
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       16     150
   16  4.95600E+00  4.13500E+00  1.05780E+01
  150  4.38400E+00  3.71300E+00  1.03550E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      152      15
  152  4.79000E+00  3.73400E+00  8.80800E+00
   15  4.43900E+00  3.75600E+00  9.28400E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       15      62
   15  4.43900E+00  3.75600E+00  9.28400E+00
   62  4.21300E+00  3.31200E+00  9.47500E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       12     207
   12  5.31500E+00  4.78100E+00  5.80300E+00
  207  5.63800E+00  4.60700E+00  5.31500E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      151      39
  151  3.27300E+00  3.45000E+00  9.23200E+00
   39  3.46800E+00  2.61800E+00  9.18500E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      151     116
  151  3.27300E+00  3.45000E+00  9.23200E+00
  116  2.59700E+00  2.90000E+00  9.53600E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      168      34
  168  6.56100E+00  4.52400E+00  5.18900E+00
   34  6.35700E+00  3.74800E+00  5.35400E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      168     103
  168  6.56100E+00  4.52400E+00  5.18900E+00
  103  7.05900E+00  4.19700E+00  4.83600E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       57     117
   57  4.50300E+00  1.84500E+00  9.53000E+00
  117  3.80000E+00  1.85700E+00  9.70800E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      199     142
  199  1.93500E+00  7.39000E+00  1.14500E+01
  142  1.67300E+00  7.27900E+00  1.22390E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       35     169
   35  4.75700E+00  5.49400E+00  4.57000E+00
  169  5.22900E+00  4.76100E+00  4.49000E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      101     181
  101  4.97300E+00  2.58300E+00  5.99200E+00
  181  5.30200E+00  1.77600E+00  6.11100E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      181     102
  181  5.30200E+00  1.77600E+00  6.11100E+00
  102  4.99900E+00  1.26800E+00  6.76500E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      226      26
  226  9.23600E+00  2.33500E+00  1.38350E+01
   26  8.94100E+00  1.76200E+00  1.41230E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       85     179
   85  1.00220E+01  3.26800E+00  1.43880E+01
  179  9.98600E+00  2.39300E+00  1.44790E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       80     178
   80  9.56100E+00  4.13700E+00  1.52920E+01
  178  1.00360E+01  4.86800E+00  1.54080E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      178      79
  178  1.00360E+01  4.86800E+00  1.54080E+01
   79  1.05840E+01  4.93500E+00  1.60910E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      166     206
  166  3.54600E+00  8.25000E-01  6.20900E+00
  206  3.57400E+00  2.48000E-01  6.92600E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      166     167
  166  3.54600E+00  8.25000E-01  6.20900E+00
  167  3.16400E+00  5.45000E-01  6.61000E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      179      86
  179  9.98600E+00  2.39300E+00  1.44790E+01
   86  1.06720E+01  1.95700E+00  1.48160E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms       96     180
   96  1.31900E+01  8.09800E+00  7.39000E+00
  180  1.29360E+01  8.00800E+00  6.55300E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      180      95
  180  1.29360E+01  8.00800E+00  6.55300E+00
   95  1.35060E+01  8.16700E+00  5.90100E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      206     167
  206  3.57400E+00  2.48000E-01  6.92600E+00
  167  3.16400E+00  5.45000E-01  6.61000E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      143     200
  143 -9.70000E-02  5.74800E+00  6.86200E+00
  200 -6.62000E-01  5.34300E+00  7.33400E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      162     204
  162  1.17990E+01  8.22100E+00  1.44600E+01
  204  1.25300E+01  8.67700E+00  1.41230E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      129     184
  129  5.74000E-01  4.96500E+00  1.37990E+01
  184  2.11000E-01  4.22900E+00  1.34780E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      183     124
  183  4.62200E+00  2.38800E+00  1.58030E+01
  124  5.27700E+00  1.82000E+00  1.56510E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      183     123
  183  4.62200E+00  2.38800E+00  1.58030E+01
  123  3.98000E+00  2.17800E+00  1.63630E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      182     114
  182  2.46900E+00  2.13800E+00  4.13400E+00
  114  2.68500E+00  2.69100E+00  3.48300E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      182     113
  182  2.46900E+00  2.13800E+00  4.13400E+00
  113  2.50900E+00  1.26800E+00  4.00100E+00
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      160     203
  160 -3.97000E-01  8.66400E+00  1.39840E+01
  203 -5.53000E-01  8.86500E+00  1.48640E+01
 Run continues in case you really meant it.
 WARNING:  TWO ATOMS VERY CLOSE TOGETHER.  CHECK INPUT.
 atoms      203     161
  203 -5.53000E-01  8.86500E+00  1.48640E+01
  161 -9.69000E-01  8.22800E+00  1.53400E+01
 Run continues in case you really meant it.
 Calculating potentials ...
    free atom potential and density for atom type    0
    free atom potential and density for atom type    1
    free atom potential and density for atom type    2
    free atom potential and density for atom type    3
    free atom potential and density for atom type    4
    free atom potential and density for atom type    5
    initial state energy
    overlapped potential and density for unique potential    0
    overlapped potential and density for unique potential    1
    overlapped potential and density for unique potential    2
    overlapped potential and density for unique potential    3
    overlapped potential and density for unique potential    4
    overlapped potential and density for unique potential    5
    muffin tin radii and interstitial parameters
 FOLP for POTENTIAL type   4 is too big.
 Reduce overlap using FOLP and rerun
MOVRLP-1

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Spline range and FT range

Hi everyone,

While I was processing my data, I found that the FT features are changing as I change the spline range.

I think the change is severe as my data contain a lot of noises at high-k regions (above 12k).

The change is remarkable even when FT range is fixed and even when the spline range is far from the low and high limits of FT range.

When data are imported into athena, the defalut values for spline ranges from 0 to the end of measured data and the high limit of FT range is set to  a value of the high limit of spline range minus 2.

There must be a relationship.

Could anyone explain these things and general rules for setting the spline range?

Thank you in advance.

 

Best wishes,

Kug-Seung Lee

Kug-Seung Lee, Ph. D.
Staff Scientist
8C Nano Probe XAFS Beamline
Pohang Accelerator Laboratory

Pohang 790-784, Republic of Korea

Office: +82-54-279-1522
Fax: +82-54-279-1599
C. P.: +82-10-6419-7801
Researcher ID: http://www.researcherid.com/rid/D-7088-2011

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Sven L. M. Schroeder | 23 Aug 17:32 2015

Academic Career Opportunity in X-ray Spectroscopy at the University of Leeds

Dear colleagues

I would like to advertise an exciting career opportunity for an X-ray spectroscopist at the University of Leeds. Leeds is one of the top 10 research-intensive Universities in the UK. Through our international academic recruitment programme ( http://250greatminds.leeds.ac.uk )  we wish to consolidate our strategic relationship with Diamond Light Source by appointing a

University Academic Fellow in Structure-Function Determination in Complex Soft Matter Systems

Chemical product and process engineering can now take advantage of structure analysis with a broad range of X-ray techniques that have become available at the UK’s synchrotron radiation source, DIAMOND. The focus of the research is to determine structure information across length scales, ideally in situ under process conditions, and from molecular to macroscopic dimensions, and to combine such information with multi-scale models to generate a seamless understanding of the relationships between microstructure, processing conditions and product performance.  The Fellowship is an exciting opportunity for an engineer or physical scientist with an interest in determining structural/performance relationships in complex products, particularly soft matter systems, with synchrotron radiation techniques.

Salary: 

£38,511 to £45,954

Closing Date: 

Wednesday 30 September 2015

Reference: 

ENGPE1026

 

Career Pathway: Successful completion of a 5 year probationary period leading to appointment to Grade 9, Associate Professor.

More particulars are available at:

https://jobs.leeds.ac.uk/Upload/vacancies/files/2719/ENGPE1026 - UAF in Structure-Function Determination in Complex Soft Matter1.pdf

For informal enquiries about the role please feel free to contact me as per details below.

 

--

Sven L. M. Schroeder

Royal Academy of Engineering Bragg Centenary Chair

School of Chemical and Process Engineering | Institute for Particle Science and Engineering (IPSE)  | University of Leeds | Leeds LS2 9JT | UK

Room 2.22  |  Engineering Building

T   +44 (0)113 343 2401  |  PA/secretary (Kirn Jutlla) +44 (0)113 343 2404  |  F +44 (0)113 343 2384

E   s.l.m.schroeder-BEzM0k5Odur10XsdtD+oqA@public.gmane.org  | W  https://www.engineering.leeds.ac.uk/people/staff/s.l.m.schroeder

 

 

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Debora Meira | 19 Aug 10:50 2015
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XANES simulation K-edges

Dear all,

I'd like to know which kind of concern I should have for feff to simulate the XANES for K-edges. I'm asking because I'm trying to simulate Sn K-edge and I have around 30 eV energy shift for the edge position. Can it be related with a wrong parameter for one of the cards?

Thank you, Debora Meira
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herve muguerra | 14 Aug 10:41 2015
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La2Zr2O7 EXAFS fitting

Dear All,

First of all, I am still very new in EXAFS analysis, so please excuse me 
for any misunderstandings.

My sample is a crystalized La2Zr2O7 thin layer (thickness = 100 nm) on a 
NiW substrate and we have realized EXAFS measurements by grazing angle 
under primary vacuum at Lathanum L3 edge (ESRF, Grenoble, France).

My objectives are to establish the local distortions due to the 
different constraints in the oxide thin layer.

The La2zr2O7 crystalized in a pyrochlore structure (SG = Fd-3m ; a = 
10.78A).
First scattering path
La-O2.1                                2.3352A
La-O1.1                                2.6453A

But I have a problem: I observe the first peaks at 1.28A and 1.80A on 
the EXAFS spectra as a function of R.

How do you explain this feature?

Can you point me in the right direction for these issues?

I attached the project file La_80_LZO_1000.prj of my sample:
LAHM045 to LAHM50 = 6 different scans
La_80_LZO_1000 = Data merge

Thanks

Best regards

Hervé Muguerra
Attachment (La_80_LZO_1000.prj): application/octet-stream, 22 KiB
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Fowler, Joseph W. | 11 Aug 22:49 2015

MacPorts now contains Demeter 0.9.22 (and requires Perl 5.22)

Dear Bruce:


Wait a minute! In fact, I updated the Mac Ports package demeter within the last two weeks to use Demeter version 0.9.22. Mac users might want to use the latest version and should consider doing a "port self update && port upgrade demeter". 


Users who installed the development version port called demeter-devel will also land on 0.9.22 if they upgrade to the latest.

Note that the latest Mac Ports version is known as 0.9.22_1, where the revision number _1 corresponds to the upgrade from Perl 5.16 to 5.22 (which the MacPorts team is pushing on). For many users, there will be numerous dependency upgrades when you upgrade to 0.9.22_1, but I found they took only a few minutes in my particular case. This change in Perl versions could conceivably cause problems, but I haven't heard of any.

Best wishes,
Joe Fowler
(MacPorts maintainer for demeter)

From: Bruce Ravel <bravel-IGkKxAqZmp0@public.gmane.org>
Sent: Tuesday, August 11, 2015 6:55 AM
To: XAFS Analysis using Ifeffit
Subject: Re: [Ifeffit] Energy shift after deglitch
 

I don't see the behavior you describe when I follow your recipe.
Perhaps it got fixed when I fixed this fellow's issue...?

http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2015-May/012496.html

Of course, the Mac package is a fair bit behind at this point.

B

On 08/06/2015 06:10 PM, George Sterbinsky wrote:
> Hello,
>
> I am writing to report a bug in Athena running on OSX 10.10.4. Here are
> the steps to reproduce the problem. I'm not sure that all steps are
> necessary.
>
> 1. Open Athena and import the attached project, which contains two
> groups that are both marked.
> 2. Change plot range to plot from -30 to 30 eV.
> 3. Select the "deglitch and truncate" window.
> 4. Select group "Ref data.merge".
> 5. In deglitch many points, set margin to 0.05, Emin to -24, and Emax to
> -20.
> 6. Click replot margins.
> 7. Click remove points.
> 8. Click return to main window.
> 9. Click the derivative check box to plot marked groups as normalized
> derivative.
> 10. Click mu(E) button to plot marked groups as derivative of mu(E).
>
> When the last step is done the groups appear to shift with respect to
> each other. One can switch between Normalized and mu(E) and see the
> shift come and go.
>
> Thank you,
> George
>
>
>
> _______________________________________________
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--
  Bruce Ravel  ------------------------------------ bravel-F56T3RlMPU4@public.gmane.orgv

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 535A
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/

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pushkar shejwalkar | 10 Aug 11:11 2015
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Unable to install demeter

Dear Users and Bruce,
  I am trying to install demeter with 64bits for my windows 7 professional laptop {4 gb ram, ample amount of free memory} . I tried downloading using both available links 1( on the left side of the window with the button for 64 bits and then by cliking the link in the text too. For some reason it didnt downloaded the file. I tried using 32 bits just to check and it started downloading * i didnt finish that and canceled the download since I dont need that one.
Following error message appeared in the window
This XML file does not appear to have any style information associated with it. The document tree is shown below.
Could anyone help me with this whats wrong? I am using demeter on my other laptop and its working perfectly.
Best
Pushkar

--
Best Regards,
Pushkar Shejwalkar.
Post-doctoral -Researcher,
Tokyo Engineering University,
Sapporo,
Japan

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Anatoly I Frenkel | 8 Aug 00:06 2015

XAFS short course in BNL on Nov 5-7: Save the date

Dear IFEFFIT subscribers:

 

Please save the dates, Nov. 5-7, 2015, of the annual XAFS short course in Brookhaven National Laboratory. As many of you may know, we vary our themes from year to year, and we also vary the target levels for participants from beginners to intermediate to advanced. This year the target level for participants is "advanced", as suggested by the course title "Advanced topics in XAFS data modeling". It is similar in scope to our other courses on this subject (the latest one was offered in Brookhaven in 2010) that are available online:

 

http://www.yu.edu/scc/workshops-courses/

 

This time the course will be divided in two parts: non-linear analysis methods (FEFF theory-based) and linear methods (based on methods of multivariate analysis and linear algebra such as LCF, PCA and MCR-ALS).

 

Nov. 5 (Thursday) and Nov. 6 (Friday) will be devoted to lectures and demonstrations of the software.

Nov. 7 (Saturday) will be practical session,  in which registered participants will practice problem solving methods discussed in the previous days.

 

Confirmed instructors are: Alain Michalowicz, Stephen Wasserman, Faisal Alamgir, Scott Calvin and Anatoly Frenkel. A full list of instructors and additional information on the course will soon appear on BNL web site. Participation in the practical data analysis session will be limited to 30 registered attendees, although auditors are welcome to attend the lectures and demonstrations on Thursday and Friday.

 

For any inquiries please use contact info on the course web that will soon come online.

 

Best regards,

 

Anatoly Frenkel

Yeshiva University

 

 

Anatoly Frenkel, Ph.D.
Professor and Chair, Department of Physics, Yeshiva University
245 Lexington Avenue, New York, NY 10016
Spokesperson, Synchrotron Catalysis Consortium http://yu.edu/scc
Office: (212) 340-7827, Lab: (631) 344-3013, Email: anatoly.frenkel-OKzqDoqOkpk@public.gmane.org
 
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