Re: [Ifeffit] demeter installation in OSX El Capitan

[Matt Newville]

Demeter 0.9.24 does work for me on El Capitan (10.11.5).  In fact, I did a
sudo port upgrade outdated

and many packages updated, and and Demeter still lauches and seems to run.

Yuan, you say you upgraded to 10.11.  Does that mean you had Macports /
Demeter working on 10.10 and it failed to work when you upgraded? If so,
you might try completely uninstalling Macports and starting over.

Just for fun (well, maybe chasing Pokemon or over-analyzing Brexit is more
your thing, but this works for me), I just moved my "/opt" and
"/Applications/Macports" folder, reinstalled the Macports package, and then
re-installed with
sudo port install demeter

(I think you don't need to specify xorg-server) and it magically worked.

So, maybe try uninstalling and installing again?   Or maybe try installing
without xorg-server?

--Matt
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Re: [Ifeffit] demeter installation in OSX El Capitan

[Ping, Yuan]

Hi Joe,

Thanks for your reply. In my first email I forgot to mention that I did install 
MacPorts-2.3.4-10.11-ElCapitan.

Yuan



On 7/21/16, 11:27 AM, "Ifeffit on behalf of Fowler, Joseph W. (Assoc)" 
mailto:ifeffit-boun...@millenia.cars.aps.anl.gov>
 on behalf of joe.fow...@nist.gov> wrote:

Dear Yuan,

Thanks for the log file, but I’m afraid I don’t know what your Mac Ports 
problem is. The log file indicates a failure to fetch the archive at all. After 
waiting a day, did the problem go away?

My workplace has lots of rules about how and when to upgrade to El Cap. As a 
result, I have not done it myself yet. Have you visited the Mac Ports team’s 
page on OS X 10.11? https://trac.macports.org/wiki/ElCapitanProblems  There are 
no specific problems mentioning libcxx, I notice. Did you remember to 
re-install Mac Ports itself? If not, then problems are inevitable. Also, are 
Xcode and its command-line tools both updated to match the OS?

If you’ve followed all the upgrade instructions and cannot install libcxx, then 
I think you have a Mac Ports problem and should look to that project’s issue 
tracker (possibly filing an issue yourself).

Best wishes,
Joe Fowler
NIST Boulder Labs

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[Ifeffit] demeter installation in OSX El Capitan

[Fowler, Joseph W. (Assoc)]

Dear Yuan,

Thanks for the log file, but I’m afraid I don’t know what your Mac Ports 
problem is. The log file indicates a failure to fetch the archive at all. After 
waiting a day, did the problem go away?

My workplace has lots of rules about how and when to upgrade to El Cap. As a 
result, I have not done it myself yet. Have you visited the Mac Ports team’s 
page on OS X 10.11? https://trac.macports.org/wiki/ElCapitanProblems  There are 
no specific problems mentioning libcxx, I notice. Did you remember to 
re-install Mac Ports itself? If not, then problems are inevitable. Also, are 
Xcode and its command-line tools both updated to match the OS?

If you’ve followed all the upgrade instructions and cannot install libcxx, then 
I think you have a Mac Ports problem and should look to that project’s issue 
tracker (possibly filing an issue yourself).

Best wishes,
Joe Fowler
NIST Boulder Labs

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Re: [Ifeffit] demeter installation in OSX El Capitan

[Ritimukta Sarangi]

I don't think it works on el capitan

Sent from my iPhone

> On Jul 20, 2016, at 22:37, Ping, Yuan  wrote:
> 
> Dear all,
> 
> I recently upgraded my mac to OSX El Capitan, and tried to install demeter 
> following the steps at http://bruceravel.github.io/demeter/
> 
> XQuartz 2.7.9 (xorg-server 1.17.4), Xcode 7.3.1, command line tools, “sudo 
> port -v self update”, “port upgrade outdated” were all OK. When I tried “sudo 
> port install xorg-server demeter”, it showed:
> 
> --->  Computing dependencies for xorg-server
> --->  Cleaning xorg-server
> --->  Computing dependencies for demeter
> --->  Dependencies to be installed: ifeffit libgcc cctools llvm-3.8 libcxx 
> libffi llvm_select gmp isl ld64 ld64-latest libmpc mpfr pgplot gcc5 ... (a 
> long list)
> 
> Then after many attempts to fetch libcxx-3.7.1_0.darwin_15.x86_64.tbz2 from 
> various websites, it showed:
> 
> Error: org.macports.archivefetch for port libcxx returned: archivefetch 
> failed for libcxx @3.7.1_0
> Error: Failed to install libcxx
> Please see the log file for port libcxx for details:
>
> /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_libcxx/libcxx/main.log
> 
> The log file is attached. What should I do to fix it? Any suggestion will be 
> appreciated.
> 
> Thanks.
> Yuan
> 
> 
> 
> 
> 
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Re: [Ifeffit] determining reasonable fitting parameters

[Bruce Ravel]

On 07/20/2016 06:59 PM, Neil M Schweitzer wrote:

In terms of the DWF’s in general, what value is considered too high? I
know the DWF’s have a component that relates to temperature induced
disorder in the scattering shell and a component that relates to
physical disorder in the scattering shell, but what value would be
considered too big for a sample measured at room temperature. I have
seen values as high as 0.03 and 0.04 in presentations (sorry, no
references) but these seems too large to me. At some point, if the
sample is disordered enough, it seems like EXAFS is no longer an
appropriate characterization tool to use. What value of DWF would that
represent (for a sample measured at room temperature)?


This one is a bit easier than your first question, so I'll take a stab 
as I am drinking my morning coffee.


As you have certainly noticed, defensible sigma^2 values tend to be 
0.00something.  Values for sigma^2 that are 0.0something tend to be very 
unrobust parameters in the sense that they cause so much attenuation 
that they more-or-less serve to remove the scattering path from the fit. 
 It is likely that the uncertainty will be similarly large in a fit 
like that.


One point I often try to get across when answering questions here is 
that often things that are presented as problems are actually useful 
information.  That is, a sigma^2 of 0.0something is trying to tell you 
that the Fourier components represented by the path are not represented 
(or represented very weakly) in the actual data.  A big sigma^2 is 
Artemis' way of suggesting one of your assumptions about the structural 
model might not be quite right.


In that case, it is likely that the fit will not change -- and might 
improve by virtue of reducing the count of guess parameters by one -- if 
you remove the path and remove the parameter.


To look at it another way: a result of "it's too disordered to measure" 
*is* a result.  It may not be quantitative.  It may not be what the boss 
is looking for.  But it's honest and it is a result.


HTH,
B


--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 743, Room 114
 Upton NY, 11973

 Homepage:http://bruceravel.github.io/home/
 Software:https://github.com/bruceravel
 Demeter: http://bruceravel.github.io/demeter/
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Re: [Ifeffit] determining reasonable fitting parameters

[Bruce Ravel]

On 07/20/2016 06:59 PM, Neil M Schweitzer wrote:

I found a bug in the log files in the history window. I am running
Demeter 0.9.21 on Windows 7. When I generate a new fit, if I change the
k-range of the fit, the k-range of previous fits in the history window
will also change to the current range (e.g. fit 19 was run from 2.1-9.3,
as shown in the data window. Fits 14-16 were run in smaller ranges).
What’s even stranger, is if I go to a very old fit (i.e. fit 1 or 2 in
the project file) and then go back to the new fit, the log file will
report the k-range from the earlier fit, not the current fit. Obviously,
this is making it very difficult to keep track of fits generated with
different k-ranges. I have not tested to see if the R-range behaves
similarly.


Neil,

Thanks for reporting this.  The fit history mechanism is probably not 
one of the better tested parts of Artemis.  I'll look into it soon.


B

--
 Bruce Ravel   bra...@bnl.gov

 National Institute of Standards and Technology
 Synchrotron Science Group at NSLS-II
 Building 743, Room 114
 Upton NY, 11973

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