Hi, I am hoping someone can explain to me how to run Feff 7 on a mac (OSX
version 10.5.8) starting from the feff702.f file.
Thank you,
George
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On Oct 27, 2010, at 12:43 PM, George Sterbinsky wrote:
Hi, I am hoping someone can explain to me how to run Feff 7 on a mac (OSX
version 10.5.8) starting from the feff702.f file.
Thank you,
George
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On Wed, Oct 27, 2010 at 12:43 PM, George Sterbinsky
georgesterbin...@u.northwestern.edu wrote:
Hi, I am hoping someone can explain to me how to run Feff 7 on a mac
(OSX
version 10.5.8) starting from the feff702.f file.
Thank you,
George
Is it possible that I need to download and install the gfortran-4.2.3.dmg
file in addition to gfortran-42-5577.pkg file? Any suggestions as to what to
try would be appreciated.
thanks,
George
On Tue, Nov 2, 2010 at 1:59 PM, George Sterbinsky
georgesterbin...@u.northwestern.edu wrote:
Matt
? Is it
possible that gfortran-42-5577.pkg placed it somewhere else?
George
On Wed, Nov 3, 2010 at 3:12 PM, Matt Newville newvi...@cars.uchicago.eduwrote:
Hi George,
On Wed, Nov 3, 2010 at 2:07 PM, George Sterbinsky
georgesterbin...@u.northwestern.edu wrote:
Is it possible that I need
wrote:
Hi George,
On Wed, Nov 3, 2010 at 2:37 PM, George Sterbinsky
georgesterbin...@u.northwestern.edu wrote:
I've also noticed that there is not a file or directory called
gfortran
in
'/usr/local/bin'. This is what made me think I may also need to
install
the
gfortran
Hi, I am wondering what is the best way to uninstall iXAFS version 2.1.1 for
Leopard before installing the new version. Is it sufficient to just drag
iXAFS.app to the trash or is there a better way to make sure everything gets
removed?
Thank you,
George
,
George
On Mon, Nov 29, 2010 at 10:37 AM, Jeff Terry ter...@iit.edu wrote:
That should work fine. Alternately, you the new version should overwrite
the old if you drag it to the Applications folder.
Sent from my iPhone
On Nov 29, 2010, at 9:05 AM, George Sterbinsky
georgesterbin
Also, for anyone who just wants to see the difference in the two data sets
I've attached a figure.
George
On Thu, May 12, 2011 at 1:23 PM, George Sterbinsky
georgesterbin...@u.northwestern.edu wrote:
Hello,
I've noticed an odd behavior in Athena and Artemis and I was hoping someone
could
Hi Lisa,
I'm not very familiar with PbSO4, so I'm not sure if I can help, but your
email immediately brought some questions to mind.
First, did you import the same information into atoms and the crystal
structure program? The way you worded your message made me think that the
crystal structure
Hi Lisa,
Let me just mention one situation I have encountered using atoms, and how I
resolved it. I am not sure if this is the result of a bug or not, but
perhaps you can try applying the approach I took to your own situation and
see if it can resolve your problem.
The issue I encountered was
by somebody else. Or there is a mistake in
the paper.
Anyway. Thanks for sharing this idea.
Lisa
Date: Thu, 26 May 2011 11:41:08 -0400
From: George Sterbinsky georgesterbin...@u.northwestern.edu
To: XAFS Analysis using Ifeffit ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit
Hello,
When fitting data in Artemis with the other k weight box checked and the
kw = 1, 2, or 3 boxes unchecked, I find that the log file lists k-weight =
1, kw, where kw is the value I entered into the other k weight text box.
If I choose 0 as the other k weight, then the log file lists k-weight
Thanks Bruce.
George
On Tue, Sep 20, 2011 at 3:48 PM, Bruce Ravel bra...@bnl.gov wrote:
On Tuesday, September 20, 2011 03:44:55 pm Bruce Ravel wrote:
I have not explored this issue in the new Artemis, but if is exists it
will be fixed before the next Demeter release.
FWIW, I tested this
Hello,
I am wondering what values Artemis/feffit use for kmax and kmin when
calculating the number of independent points (Nidp) for a fit done in
R-space, where according the feffit document, Nidp = { [2*(kmax -
kmin)*(Rmax-Rmin) / pi] + 2}, and kmax and kmin define the fitting range. I
have
given for independent points in the log fie?
Thank you,
George
On Fri, Oct 7, 2011 at 1:04 PM, George Sterbinsky
georgesterbin...@u.northwestern.edu wrote:
Hello,
I am wondering what values Artemis/feffit use for kmax and kmin when
calculating the number of independent points (Nidp) for a fit
Sorry, the log file is from Artemis, not Athena...
On Mon, Oct 10, 2011 at 10:35 AM, George Sterbinsky
georgesterbin...@u.northwestern.edu wrote:
Hello,
Since I haven't received a response to my previous question, I just wanted
to make sure I asked it clearly. To elaborate, I am attaching
Bruce, Matt, and Jeremy,
Thank you for explaining this. Your responses are much appreciated.
George
On Mon, Oct 10, 2011 at 11:35 AM, Bruce Ravel bra...@bnl.gov wrote:
On Monday, October 10, 2011 10:35:12 am George Sterbinsky wrote:
Since I haven't received a response to my previous
Tony,
Have you checked to see if the directories referenced in your error
messages actually exist?
I am running iXAFS (according to the about iXAFS menu it is version 2
(2.2)) on mac OSX 10.5.8. One thing I noticed is that the directory
referenced in your error message,
Tony, You ask are there hidden files I should remove as well that aren't
removed...? I do find a Perl folder in my Library folder. I'm not sure
if this was installed by iXAFS or affects iXAFS...
George
On Thu, Feb 2, 2012 at 8:18 PM, Tony Kelly tkell...@gmail.com wrote:
This will make me
Hi list members,
I am attempting to install ifeffit on mac book running Lion (10.7.4). I
have downloaded and installed xcode and gfortran. I downloaded the iffeffit
package from github. I then cd into .../Downloads/newville-ifeffit-30644e
and run
sudo ./PGPLOT_install
I get the following error:
Hello,
Has anyone been able to install Demeter on windows8?
When I try to open Athena I get the message in attached screen shot.
I tried reinstalling as suggested by the message, which did not help. One
thing I noticed however was that Perl was not removed by the built in
Demeter uninstaller.
Hi All,
Athena seems to be running now. It may have just been necessary to reboot
the system, though I also reinstalled again, so I'm not certain exactly
what fixed it.
Thank you,
George
On Tue, Nov 13, 2012 at 5:58 PM, George Sterbinsky
georgesterbin...@u.northwestern.edu wrote:
Hello
Hello,
I am observing some behavior in (D)Athena that I do not understand, and I
was hoping someone could explain it to me. I have attached a project file
to illustrate my question. The first two groups in the file have been
normalized such that mu(E) and norm(E) are identical. I then merged
do what you want. The solution is to go find the find the right tool
for the job. Or, if it doesn't exist, write it yourself.
B
On Thursday, December 06, 2012 10:59:55 AM George Sterbinsky wrote:
Hello,
I am observing some behavior in (D)Athena that I do not understand, and I
I am writing to make you aware of what I believe to be a bug in (D)Athena.
To demonstrate the problem, I have attached a project file containing two
groups. Both groups have the same energy range but were measured with
slightly different point spacings. Attempting to merge the two groups
results
or have you
reinterpolate one spectrum?
Chris Patridge
Christopher J. Patridge, PhD
NRC Post Doctoral Research Associate
Naval Research Laboratory
Washington, DC 20375
Cell: 315-529-0501
On 2/26/2013 6:55 PM, George Sterbinsky wrote:
I am writing
Thanks Bruce
On Wed, Feb 27, 2013 at 8:28 AM, Bruce Ravel bra...@bnl.gov wrote:
On Tuesday, February 26, 2013 06:55:21 PM George Sterbinsky wrote:
I am writing to make you aware of what I believe to be a bug in
(D)Athena.
To demonstrate the problem, I have attached a project file
Hello,
I have attached an (D)Athena project with containing two groups, imported
as a primary data set and a reference. The groups were therefore imported
on the same energy grid. However, when plotted, the energy values of the
data points for the two groups are clearly shifted with respect to
The question of whether it is appropriate to use flattened data for
quantitative analysis is something I've been thinking about a lot recently.
In my specific case, I am analyzing XMCD data at the Co L-edge. To obtain
the XMCD, I measure XAS with total electron yield detection using a ~70%
left or
of the MCD peaks
will be at least a little corrupted even if the pre- and post-edge
spectra are taken into account. I don't know what to do about this. Did
you try asking Elke?
mam
On 5/15/2013 11:52 AM, George Sterbinsky wrote:
Hi Matthew,
On Wed, May 15, 2013 at 1:20 PM, Matthew
Hi Bruce,
That seems to do the trick for me as well. Thanks!
George
On Tue, Sep 24, 2013 at 5:44 PM, Bruce Ravel bra...@bnl.gov wrote:
On 09/20/2013 11:53 AM, George Sterbinsky wrote:
Hello,
I am writing to report what I believe to be a bug in Athena. I am using
Demeter 0.9.18
Hello,
I am writing to report what I believe to be a bug in Athena. In the
attached project, there are two groups, a main group and a reference group.
Changing the name of the first group does not change the name of the
reference group. Changing the name of the reference group separately
doesn't
Hello,
I am writing to report a crash of Athena 0.9.18 running on Ubuntu 12.04 as
a virtual machine. The terminal output is below. Let me know if I can
provide any additional information.
Thanks,
George
parallels@parallels-Parallels-Virtual-Platform:~$ dathena
Attribute (bkg_nor1) does not pass
...@bnl.gov wrote:
On 10/27/2013 02:43 PM, George Sterbinsky wrote:
Hello,
I am writing to report a crash of Athena 0.9.18 running on Ubuntu 12.04
as a virtual machine. The terminal output is below. Let me know if I can
provide any additional information.
At the command line, type denv
Hi Bruce,
I checked the demeter.ini file and nor1 is set to 150. In fact, I don't see
any values ending in a trailing decimal point in this file.
I have found however that I can reliably crash Athena by opening up a
project, and trying to manually type a value (seemingly any value) for the
start
Hi Florian,
The acronyms stand for
Scan Region Boundary
Scan Region Step Size
Seconds Per Point
Best,
George
On Tue, Nov 5, 2013 at 6:51 AM, daltonabd...@gmail.com
daltonabd...@gmail.com wrote:
Hello, Florian.
Welcome to the list!
I watched Bruce's video a while ago and I can not
Hi Frank,
I installed Athena on OSX 10.8.5 using Macports. The error given below
prints to the terminal when I run Athena, and Athena does not generate any
plots. If there is any further information I can provide that would be
helpful, let me know.
Graphics::GnuplotIF : cannot find environment
Hello,
I am writing with a general XAS question. It does not necessarily pertain
to Ifeffit, however, I think the topic is something some, maybe most, list
members will be knowledgeable about. So it seems like this list is a good
place to post this question.
On to the question. I have attached a
with the fit to get rid of the
shifting to left of the peaks.
Thanks,
George
I admit that I've never done soft X-ray fluorescence, so my ideas come
from hard X-ray experience, which may not totally apply.
mam
On 3/31/2014 3:01 PM, George Sterbinsky wrote:
Hello,
I am writing
by an inaccurate attempt at reading the energy scale.
Also, I somehow didn't read correctly the branching ratio from Hephaestus.
mam
On 3/31/2014 8:57 PM, George Sterbinsky wrote:
Hi Matt,
Thanks for your reply. Please see below.
On Mon, Mar 31, 2014 at 8:10 PM, Matt Newville
newvi
. Newville, or
whoever wrote the program.
mam
On 4/1/2014 9:56 AM, George Sterbinsky wrote:
Hi Matthew,
Hephaestus shows the strength of the Ll emission to be about 10% of the
La2 emission. When fitting the spectrum as a sum of Gaussians, I find that
the area of of the Gaussian used
Hello,
I am trying to learn to use Demeter following The Demeter Programmer Guide.
When I attempt to run the first example script in the importing data
section I get the following error message:
Graphics::GnuplotIF (object 1): problem closing communication to gnuplot
I also see the plot window
put
in a pause. And you get to look at the plot before it vanishes!
B
On 04/11/2014 06:45 PM, George Sterbinsky wrote:
Hello,
I am trying to learn to use Demeter following The Demeter Programmer
Guide. When I attempt to run the first example script in the importing
data section I get
Hi Bruce and Alison,
I am able to confirm the behavior reported by Alison (both bigger and
lesser problems) on OSX 10.8.5. Pressing the transfer displayed path
button causes Artemis to crash and the message below to print to the
terminal.
2014-04-18 11:18:26.309 perl5.16[1309:707] *** WARNING:
Hello,
I am running Athena 0.9.20 on OSX 10.8.5. Selecting the difference spectra
tool from the drop-down menu causes Athena to crash and the following
message to print to the terminal.
Usage: Wx::ComboBox::GetClientData(THIS, n) at
Hello,
When I attempt to open Artemis on OSX Yosemite (10.10.2) the error message
copied below prints to the terminal. The initial image that indicates
Artemis is opening does appear, although Artemis fails to open. Athena and
Hephaestus open without error. Any suggestions as to how this could be
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
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
people's changes.
Joe
--
*From:* George Sterbinsky georgesterbin...@u.northwestern.edu
*Sent:* Tuesday, August 11, 2015 8:27 PM
*To:* XAFS Analysis using Ifeffit
*Subject:* Re: [Ifeffit] MacPorts now contains Demeter 0.9.22 (and
requires Perl 5.22)
Hi Joe
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
On Thu, Nov 12, 2015 at 8:37 PM, Matt Newville <newvi...@cars.uchicago.edu>
wrote:
> Hi George,
>
>
>
> On Thu, Nov 12, 2015 at 7:59 PM, George Sterbinsky <
> georgesterbin...@u.northwestern.edu> wrote:
>
>> Hi Matt,
>>
>> I am just guessing here, but
Hi Matt,
I am just guessing here, but Zack and Manuel both mention installing
XQuartz, whereas you mention installing xorg-server. While Demeter should
work with either, perhaps on the new OS there is a problem installing
Demeter with xorg-server and one has to go with xQuartz. Have you tried
Hi Remi,
I noticed a typo in the commands you used. "selfupdate" should be one word,
not two. Perhaps this was just a typo in your email, but if not then you
may want to try running it again. Also, I noticed that the instructions at
the Demeter website say to log out and log back in after
In the Athena preferences menu, the "gnuplot-->terminal" parameter is set
to "x11" on my system. If yours is set to something else you might try
changing it to x11.
George
On Tue, Sep 22, 2015 at 4:18 PM, Bruce Ravel wrote:
> On 09/22/2015 05:03 PM, Raimundo Lora Serrano wrote:
I've found that if the terminal value is set to wxt, it is reset to qt upon
restarting Athena, and Athena will not plot. This does not happen if the
terminal value is set to x11 or aqua.
George
On Tue, Sep 22, 2015 at 9:32 PM, Matt Newville
wrote:
> Sorry for not
Hi All,
The result I get is
/private/tmp/com.apple.launchd.a2i2wnuP2l/org.macosforge.xquartz:0 and
Athena is working fine on my system.
George
On Tue, Sep 22, 2015 at 6:50 AM, Alison Tebo wrote:
> Hi Raimundo (and Rémi),
>
> I'm not a pro here but, have you installed
Demeter::UI::Artemis::__ANON__(Wx::Frame=HASH(0x7fdb96c547c0),
Wx::CommandEvent=SCALAR(0x7fdb96c576a0)) called at /opt/local/bin/Artemis
line 47
eval {...} called at /opt/local/bin/Artemis line 47
On Fri, Jul 1, 2016 at 4:26 PM, Bruce Ravel <bra...@bnl.gov> wrote:
>
> That was the right
vel/Demeter/Fit.pm,
> near line 1263 (as the traceback indicates) you will find this:
>
> ## correct for change in energy-dependent normalization
> delete $r_attributes->{bkg_fnorm};
>
> add
>
> delete $r_attributes->{bkg_funnorm};
>
>
> B
>
Hello,
Athena crashes upon import of the attached project file. I am using the
latest release of Athena for mac (0.9.22) on OSX 10.10.5. I am able to open
the file on windows. The message that is printed to the terminal when
Athena crashes is pasted below. Please let me know if any further
Hi Bruce,
Thanks for providing a fix. The Prj.pm file on my system does not look
exactly like what you describe. Lines 260 to 268 looked like this:
next if any { $k eq $_ } qw(
bindtag deg_tol denominator detectors
en_str file frozen line mu_str
numerator old_group original_label
peak
Hello,
I am using Demeter on Mac OS X 10.11.6. I recently updated Demeter to
version 0.9.25 using the command "sudo port upgrade demeter". In Artemis,
choosing the menu item "open project or data" causes Artemis to crash. I've
pasted the information printed to the terminal below. This includes
m or indicates a fix.
Thanks again,
George
On Wed, Jan 4, 2017 at 10:05 AM, Bruce Ravel <bra...@bnl.gov> wrote:
> On 12/22/2016 12:11 PM, George Sterbinsky wrote:
>
>> I have attached an Artemis project. Upon opening the project, and
>> clicking the fit button the
Thank you Matt.
George
On Mon, May 29, 2017 at 10:02 PM, Matt Newville <newvi...@cars.uchicago.edu>
wrote:
> Hi George,
>
> On Mon, May 29, 2017 at 5:57 PM, George Sterbinsky <GeorgeSterbinsky@u.
> northwestern.edu> wrote:
>
>> Hello,
>>
>> Can a
Hello,
Can anyone explain why the values given by the ion chamber utility in
Hephaestus differ from those given for a 10 cm He filled ion chamber in
figure 3.14 of Grant Bunker's Intro to XAFS book at high energy? For
instance, figure 3.14 indicates an absorption fraction of ~3E-7 at 40 keV,
Thanks for following up Ricardo. I find the same issue when doing a fresh
install of macports and demeter on MacOS Mojave (10.14.6), so it seems the
issue is not unique to Catalina.
George
On Sat, Jan 25, 2020 at 12:23 PM Ricardo Faccio wrote:
> Dear all
>
> This is just a comment how to
Hi Ricardo,
Are you using dark mode? If you turn it off, does that fix the problem?
George
On Mon, Jan 27, 2020 at 9:36 AM Ricardo Faccio wrote:
> Dear all
>
> After installing Demeter in MacOS I am having some problems related to
> the color of fonts and background. Since they look identical
Hello,
I am trying to import an empirical standard (.es file created in Athena)
into Artemis. Upon import, Artemis crashes. This occurs with both the
latest mac and windows releases (0.9.25 on mac and 0.9.26 on windows). I
have attached an Athena project file containing the data used to generate
Hi All,
I am trying to upgrade larch from 0.9.45. Neither "conda update --all" nor
"pip install xraylarch" are updating to 0.9.47. Is a complete reinstall of
anaconda my only option?
Thank you,
George
On Tue, Mar 3, 2020 at 11:22 AM Matt Newville
wrote:
> Hi Garret,
>
>
> On Tue, Mar 3, 2020
Hello,
As is well known, EXAFS is more accurate at determining relative changes in
bond lengths than absolute changes in bond lengths due to cancelation of
systematic errors in relative comparisons. When comparing the relative
changes in bond lengths determined from EXAFS fits, as one might for a
"yeah, that could work" and also "maybe not perfectly".
> >
> > But, if I'm reading this PRL correctly, it looks like they use the
> > log-ratio method to compare sigma2 and R of spectra at the same
> > temperature but with different isotopes. Th
Hello,
When attempting to export an xdi file for a pre-edge peak fit in XAS
viewer, the error message below prints to the terminal and the xdi file is
not generated. I can provide the project file and instructions for
generating the error message if that would be helpful.
Thank you,
George
Hi Matt,
Thanks, that worked. I got an error that said something about 'asteval' on
my first try, so I also deleted that package.
George
On Sat, Apr 18, 2020 at 11:24 AM Matt Newville
wrote:
> Hi George,
>
> Sorry for the trouble. I think a fresh install is not the only option,
> but it
Hello,
Does anyone have Fe K-edge XANES from an Fe4+ reference or sample (for
example SrFeO3) that they can share?
Thank you,
George
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be saying that the parameter
> uncertainties weren't calculated correctly. It probably should not even be
> trying to estimate the uncertainty in the model. I believe it should be
> fixed in git master for larch, and I'll see about looking for this in lmfit
> too.
>
> On
ewer.
>
>
>
> On Wed, Apr 29, 2020 at 10:31 AM George Sterbinsky <
> georgesterbin...@u.northwestern.edu> wrote:
>
>> Hi Matt and all,
>>
>> Unfortunately, after a clean install of larch following the source
>> installation instructions, I am not able
Hi Matt,
Thanks for the explanation, I now see what you meant.
George
On Fri, May 1, 2020 at 6:28 PM Matt Newville
wrote:
> Hi George,
>
>
> On Thu, Apr 30, 2020 at 11:39 PM George Sterbinsky <
> georgesterbin...@u.northwestern.edu> wrote:
>
>> Hi Matt,
>
Hello,
I have observed changes in fixed parameters while running a pre-edge peak
fit in XAS Viewer. I first run a baseline fit. This provides a good match
to the data in the baseline fitting region. I would like to subtract the
baseline from the data and then numerically integrate the data. In
u finally solved this problem? I´m having the same situation when
> trying to import an empirical standard.
>
> Thank you,
>
> Mismel.
>
>
> El lun., 13 de abr. de 2020 a la(s) 11:04, George Sterbinsky (
> georgesterbin...@u.northwestern.edu) escribió:
>
>> He
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