Re: [Ifeffit] MacPorts install of Demeter

[Schima, Frank]

Hi Matt,

On Jan 27, 2014, at 1:18 PM, Matt Newville  wrote:

> Frank, All, 
> 
> Just to add my thanks and experience so far:  Thank you so much for this!  As 
> Martha and others have seen, everything with Athena seems to work fine for me 
> on 10.8.5, but Hephaestus and Artemis segfault on launching (after splash 
> screen).  
> 
> Should I try installing demeter from the git repo into the macports perl 
> location?  Or is there more to it?  Frank, would it be possible to post some 
> configuration notes?

You are welcome! There is nothing else to do. That is the state of things for 
now. Bruce should have fixes done soon for Hephaestus and Atoms at which point 
I will update the Macports version to get them. Then you can update Macports to 
get the fixes. We’re still not sure where the problem lies with Artemis. I will 
keep en eye out for a new version of perl-wx which may fix it. 


Cheers!
Frank


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] MacPorts install of Demeter

[Matt Newville]

Frank, All,

Just to add my thanks and experience so far:  Thank you so much for this!
As Martha and others have seen, everything with Athena seems to work fine
for me on 10.8.5, but Hephaestus and Artemis segfault on launching (after
splash screen).

Should I try installing demeter from the git repo into the macports perl
location?  Or is there more to it?  Frank, would it be possible to post
some configuration notes?

Thanks again,

--Matt
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Absorption-coefficient data repository?

[Matthew Marcus]

It won't calculate it accurately in the XANES region because it doesn't know 
about XANES.  What could be done is
to take the smooth parts from Hepheastus and scale by the XANES data.
mam

On 1/27/2014 10:43 AM, Scott Calvin wrote:

Hi Damon,

Hephaestus will calculate that for you. (There are other options, too, but that 
may be the simplest.)

--Scott Calvin
Sarah Lawrence College

On Jan 27, 2014, at 1:30 PM, Damon Turney  wrote:


Dear XAFS Community,

I'm looking for values of absorption coefficient (or mass absorption
coefficient) of ZnO in the XANES region of the Zn edge, but all the
publications give XANES plots in "arbitrary units", so I have no way
of knowing the absorption coefficient for ZnO.

Does anybody know a data repository where absorption coefficients are
collected?

Thanks,
Damon



--
Damon Turney PhD
Energy Institute, Department of Chemical Engineering
City University of New York
New York, NY 10031
dtur...@che.ccny.cuny.edu
office: (212) 650-5470
cell: (805) 571-3764
fax: (805) 823-4593
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit



___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] MacPorts install of Demeter

[Bruce Ravel]

On 01/27/2014 02:20 PM, Martha W Schaefer wrote:

Atoms does not open, and the following errors are produced:


I think this problem has already been fixed, but not in the version of
Demeter at Macports.  The next update should (fingers crossed) resolve
this issue.

Cheers,
B

--
 Bruce Ravel   bra...@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
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] MacPorts install of Demeter

[Bruce Ravel]

Hi Martha,

First off, I am very grateful for your civility in thanking Frank for
his hard work and selfless effort.


Athena opens and looks normal so far. I have no trouble loading data
and plotting. Yay!


Yay, indeed!  Hopefully you and others will put Athena through her
paces (some LCF, some PCA, some aligning, some merging, ...) and let
me know if things look right.

Also, if you see any places where labels don't seem to be written
properly or the spacing between controls seems weird, I'd like to see
a screenshot.

You can post such things to the mailing list or open an issue at the
github repository:

   https://github.com/bruceravel/demeter



Artemis fails (as we were warned) with segmentation fault that crashed Perl.


This one is a mystery to me.  I am eventually going to need some help
on this one.  It will involve following some peculiar instructions and
reporting back to me.  If someone would like to volunteer to help out,
that would be great.


Hephaestus also fails (as warned), in the same way.


I think I know what the problem is with Hephaestus, so hopefully the
next update will resolve that problem.


Atoms does not open, and the following errors are produced:


Thanks for the useful error reporting.  Very helpful!  I will look
into the problem.

B

--
 Bruce Ravel   bra...@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
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

[Ifeffit] MacPorts install of Demeter

[Martha W Schaefer]

First of all, thank you Frank so much for making the MacPorts install possible 
for Demeter!  I have installed it on my MacBook Pro running MacOS 10.8.5, and 
here is a short report in how well it is running.  Hope this is of use.

Athena opens and looks normal so far. I have no trouble loading data and 
plotting. Yay!

I think feff and feffit also work, but I don't know how to use the command line 
version so I haven't been able to test them yet.

Artemis fails (as we were warned) with segmentation fault that crashed Perl.
Hephaestus also fails (as warned), in the same way.

Atoms does not open, and the following errors are produced:

Attribute (txx) does not pass the type constraint because: Validation failed fo 
'Num' with value   1.000 at 
/opt/local/lib/perl5/vendor_perl/5.16.1/darwinthread-multi-2level/Moose/Exception.pm
 line 37

Moose::Exception::_build_trace('Moose::Exception::ValidationFailedForInineTypeConstraint=HASH(0x7fcb4fe83b40)')
 called at reader Moose::Exception::trae (defined at 
/opt/local/lib/perl5/vendor_perl/5.16.1/darwin-thread-multi-2leve/Moose/Exception.pm
 line 9) line 7

Moose::Exception::trace('Moose::Exception::ValidationFailedForInlineTypConstraint=HASH(0x7fcb4fe83b40)')
 called at 
/opt/local/lib/perl5/vendor_perl/5.6.1/darwin-thread-multi-2level/Moose/Exception.pm
 line 49

Moose::Exception::BUILD('Moose::Exception::ValidationFailedForInlineTypConstraint=HASH(0x7fcb4fe83b40)',
 'HASH(0x7fcb4fe839f0)') called at 
/opt/local/ib/perl5/vendor_perl/5.16.1/darwin-thread-multi-2level/Class/MOP/Method.pm
 line128

Class::MOP::Method::execute('Moose::Meta::Method=HASH(0x7fcb4ff6fac8)','Moose::Exception::ValidationFailedForInlineTypeConstraint=HASH(0x7fcb4fe83b40),
 'HASH(0x7fcb4fe839f0)') called at 
/opt/local/lib/perl5/vendor_perl/5.16.1/darin-thread-multi-2level/Moose/Object.pm
 line 56

Moose::Object::BUILDALL('Moose::Exception::ValidationFailedForInlineTypConstraint=HASH(0x7fcb4fe83b40)',
 'HASH(0x7fcb4fe839f0)') called at 
/opt/local/ib/perl5/vendor_perl/5.16.1/darwin-thread-multi-2level/Moose/Meta/Class.pm
 line282

Moose::Meta::Class::new_object('Moose::Meta::Class=HASH(0x7fcb4fe873b0), 
'HASH(0x7fcb4fe839f0)') called at 
/opt/local/lib/perl5/vendor_perl/5.16.1/darin-thread-multi-2level/Moose/Object.pm
 line 27

Moose::Object::new('Moose::Exception::ValidationFailedForInlineTypeConsraint', 
'type_constraint_message', 'Validation failed for \'Num\' with value   
.000', 'class_name', 'Xray::Crystal::Cell', 'attribute_name', 'txx', 
'value, '  1.000') called at 
/opt/local/lib/perl5/vendor_perl/5.16.1/darwin-threa-multi-2level/Moose/Util.pm 
line 51

Moose::Util::throw_exception('ValidationFailedForInlineTypeConstraint','type_constraint_message',
 'Validation failed for \'Num\' with value   1.00', 'class_name', 
'Xray::Crystal::Cell', 'attribute_name', 'txx', 'value', '  1.00') called 
at accessor Xray::Crystal::Cell::txx (defined at 
/opt/local/libperl5/site_perl/5.16.1/darwin-thread-multi-2level/Xray/Crystal/Cell.pm
 line 133 line 9
Xray::Crystal::Cell::txx('Xray::Crystal::Cell=HASH(0x7fcb4b01e998)', ' 
1.000') called at 
/opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi2level/Xray/Crystal/Cell.pm
 line 170

Xray::Crystal::Cell::geometry('Xray::Crystal::Cell=HASH(0x7fcb4b01e998)) called 
at 
/opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Xry/Crystal/Cell.pm
 line 73

Xray::Crystal::Cell::__ANON__('Xray::Crystal::Cell=HASH(0x7fcb4b01e998), 0, 0) 
called at accessor Xray::Crystal::Cell::b (defined at 
/opt/local/lib/pel5/site_perl/5.16.1/darwin-thread-multi-2level/Xray/Crystal/Cell.pm
 line 75) lie 15
Xray::Crystal::Cell::b('Xray::Crystal::Cell=HASH(0x7fcb4b01e998)', 0) 
clled at 
/opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Xray/Cystal/Cell.pm
 line 64

Xray::Crystal::Cell::__ANON__('Xray::Crystal::Cell=HASH(0x7fcb4b01e998), 0, 0) 
called at accessor Xray::Crystal::Cell::a (defined at 
/opt/local/lib/pel5/site_perl/5.16.1/darwin-thread-multi-2level/Xray/Crystal/Cell.pm
 line 69) lie 15
Xray::Crystal::Cell::a('Xray::Crystal::Cell=HASH(0x7fcb4b01e998)', 0) 
clled at 
/opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Xray/Cystal/Cell.pm
 line 144
Xray::Crystal::Cell::clear('Xray::Crystal::Cell=HASH(0x7fcb4b01e998)') 
alled at 
/opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Demetr/Atoms.pm
 line 302
Demeter::Atoms::clear('Demeter::Atoms=HASH(0x7fcb4b016358)') called at 
opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Demeter/Atoms.p 
line 316
Demeter::Atoms::read_inp('Demeter::Atoms=HASH(0x7fcb4b016358)') called 
t 
/opt/local/lib/perl5/site_perl/5.16.1/darwin-thread-multi-2level/Demeter/Atom.pm
 line 169
Demeter::Atoms::__ANON__('Demeter::Atoms=HASH(0x7fcb4b016358)', 
'atoms.np') called at constructor Demeter::Atoms::new 

Re: [Ifeffit] Absorption-coefficient data repository?

[Matt Newville]

Hi Damon,


On Mon, Jan 27, 2014 at 12:30 PM, Damon Turney wrote:

> Dear XAFS Community,
>
> I'm looking for values of absorption coefficient (or mass absorption
> coefficient) of ZnO in the XANES region of the Zn edge, but all the
> publications give XANES plots in "arbitrary units", so I have no way
> of knowing the absorption coefficient for ZnO.
>
> Does anybody know a data repository where absorption coefficients are
> collected?
>
>
Scott and Bruce gave pointers to where tables of absorption coefficients
can be found.These are per-atom, and ignore any fine structure or
chemistry effects.  XANES measurements are typically labeled as "arbitrary
units" because it is both surprisingly tricky and unnecessary for (most)
XANES or EXAFS analysis to actually have an accurate absolute measure of
the absorption coefficient (either in mass/area or inverse length).

We can easily measure XANES features at ~1% of the edge jump.   But to get
this signal we've (generally, without loss of generality) sampled the
intensity of the X-ray beam with an ion chamber that typically absorbs a
few percent of the X-rays upstream of our sample, and an ion chamber
downstream of our sample (that might absorb more of the X-rays hitting
it).  The beam travels through, and is partially absorbed by, any air paths
and other material (plastics, sample containers) as well as our sample.
Typically, the sample attenuates the beam by between a factor of 2 and a
factor of 100.  The additional stuff in the beam may attenuate by this much
as well.

We typically take "Current from upstream ion chamber" as I0 (it is NOT the
absolute flux hitting the sample) and "Current from downstream ion
chamber"  I1 (again, NOT the flux leaving the sample), and call -log(I1/I0)
"mu" -- it is not in any real units.

To get the real attenuation (thickness  * absorption coefficient) for the
sample, we'd have to take many things (some rather subtle) into account.
And because attenuation is exponential, you actually have to be pretty
careful to get this right.  On the other hand, for analyzing XANES and
EXAFS we really only care about the change in the absorption coefficient
from the element of interest, and are willing to normalize to 1 atom of the
absorbing species.   This can be tricky enough, but it means all that other
stuff cancels out.To get the absorption coefficient, you have to divide
by the sample thickness (and/or know the sample's density).   But sample
thicknesses are typically ~10 microns, and if you think you know the
average thickness of a sample to 1% of 10 microns, you must have made a
very uniform and precise sample, at least compared to what most people
study with EXAFS.

That's not to say it can't be done.  A few people, notably Chris Chantler's
group at U Melbourne have made some such measurements.   They're
challenging, and most beamlines are not set up to do this easily.

Out of curiosity, why do you need to know the (absolute) values for
absorption coefficient for ZnO?

-- 
--Matt
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Absorption-coefficient data repository?

[Bruce Ravel]

On 01/27/2014 01:30 PM, Damon Turney wrote:

Dear XAFS Community,

I'm looking for values of absorption coefficient (or mass absorption
coefficient) of ZnO in the XANES region of the Zn edge, but all the
publications give XANES plots in "arbitrary units", so I have no way
of knowing the absorption coefficient for ZnO.

Does anybody know a data repository where absorption coefficients are
collected?

Thanks,
Damon


You have ways of knowing such things.

The document for my Hephaestus program lists citations for the various
data resources available in my Xray::Absorption perl module:

  http://bruceravel.github.io/demeter/aug/hephaestus.html#credits

The original data for the various resources comes with Demeter and can
be browsed at:

  https://github.com/bruceravel/demeter/tree/master/lib/Xray/data

This is is from Matt Newville and Darren Dale and it very useful:

  https://github.com/XraySpectroscopy/XrayDB

LBL's Center for X-ray Optics is a classic resource:

  http://henke.lbl.gov/optical_constants/

B

--
 Bruce Ravel   bra...@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
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Absorption-coefficient data repository?

[Scott Calvin]

Hi Damon,

Hephaestus will calculate that for you. (There are other options, too, but that 
may be the simplest.)

--Scott Calvin
Sarah Lawrence College

On Jan 27, 2014, at 1:30 PM, Damon Turney  wrote:

> Dear XAFS Community,
> 
> I'm looking for values of absorption coefficient (or mass absorption
> coefficient) of ZnO in the XANES region of the Zn edge, but all the
> publications give XANES plots in "arbitrary units", so I have no way
> of knowing the absorption coefficient for ZnO.
> 
> Does anybody know a data repository where absorption coefficients are
> collected?
> 
> Thanks,
> Damon
> 
> 
> 
> -- 
> Damon Turney PhD
> Energy Institute, Department of Chemical Engineering
> City University of New York
> New York, NY 10031
> dtur...@che.ccny.cuny.edu
> office: (212) 650-5470
> cell: (805) 571-3764
> fax: (805) 823-4593
> ___
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

[Ifeffit] Absorption-coefficient data repository?

[Damon Turney]

Dear XAFS Community,

I'm looking for values of absorption coefficient (or mass absorption
coefficient) of ZnO in the XANES region of the Zn edge, but all the
publications give XANES plots in "arbitrary units", so I have no way
of knowing the absorption coefficient for ZnO.

Does anybody know a data repository where absorption coefficients are
collected?

Thanks,
Damon



-- 
Damon Turney PhD
Energy Institute, Department of Chemical Engineering
City University of New York
New York, NY 10031
dtur...@che.ccny.cuny.edu
office: (212) 650-5470
cell: (805) 571-3764
fax: (805) 823-4593
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Demeter on Mac OS X via Macports

[Schima, Frank]

Hey all,


Thanks for this feedback. X11 can also be installed directly through Macports. 
The port is called xorg-server. So here is the modified command to install 
Demeter with X11. Follow this with a logout and login.

sudo port install xorg-server demeter

Yes, XQuartz will work too. The Macports version will generally be newer 
because the developer at Apple responsible for XQuartz is the same person that 
keeps it updated at Macports.


Cheers!
Frank

On Jan 26, 2014, at 7:10 PM, Jeff Terry mailto:ter...@iit.edu>> 
wrote:

Glad to hear it.

Jeff

Sent from my iPhone

On Jan 26, 2014, at 7:49 PM, George Sterbinsky 
mailto:georgesterbin...@u.northwestern.edu>>
 wrote:

Hi Jeff,

That fixed the problem. Thanks for your help.

Best,
George


On Sat, Jan 25, 2014 at 3:35 PM, Jeff Terry 
mailto:ter...@iit.edu>> wrote:
Hi George,

This is a GUESS as I have not installed athena from macports.

I can't be sure as I don't know if that version of Athena uses X11 but I 
imagine that it does.

Try typing echo $DISPLAY in a terminal window and see if you get a result. If 
you don't then you may not have X11installed.

You can download X11 at http://xquartz.macosforge.org/trac

Jeff


On Jan 25, 2014, at 8:07 AM, George Sterbinsky 
mailto:georgesterbin...@u.northwestern.edu>>
 wrote:

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 variable DISPLAY

Best,
George





On Fri, Jan 24, 2014 at 3:22 PM, Schima, Frank 
mailto:frank.sch...@nist.gov>> wrote:
Hello Mac users,


I finally have launched a Mac OS X version of Demeter 0.9.18.2 on Macports. I 
have not tested it very much because I’m not actually a Demeter user. It 
builds, launches and opens some example data but beyond that, it is untested. 
If the Mac version interests you, fire up your Terminal and follow these 
instructions:

1. *Carefully* follow the steps to install Macports. 

2. Open a new Terminal window and type the following. It will take a while 
depending on your computer and network speed.

sudo port install demeter

3. When it is done, launch Athena by typing the following in Terminal. Note: 
Make sure you are in a directory you have write permission to (like your home 
directory) because it creates hidden log files at launch time.

athena

It is a known issue that artemis and hephaestus do not launch right now, but 
Bruce is working on a fix that will be added soon. I'm not going to have time 
to debug people's Macports issues when installing Demeter with Macports, but 
tech support is available on the Macports Users mailing list [1]. You should 
not need any help installing if you correctly follow the intructions. Please 
let Bruce and I know if it works for you or not after you have it installed. I 
have only tested on OS X Mavericks and Mountain Lion so far. Keep in mind that 
this is the first working release candidate of Demeter on Mac OS X, so problems 
are going to be expected.


Cheers!
Frank

[1] 


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] Ifeffit Digest, Vol 131, Issue 30

[Noffke, Louisa]

Thanks Bruce,

I had tried what Jeff had suggested and I got a response for 'echo $DISPLAY’ , 
but I’ve installed xquartz 2.7.5  now and am getting the plot window.
Cheers,
Louisa

> 
> As for the missing plot window, have you tried following Jeff's advice 
> to George from over the weekend?
> 
> B
> 
> 


___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

Re: [Ifeffit] no plot window in athena Re: Demeter on Mac OS X via Macports

[Bruce Ravel]

On 01/25/2014 05:21 PM, Noffke, Louisa wrote:


<2014-01-25 20:09:36.898 perl5.16[28306:507] CoreText performance note:
Client called CTFontCreateWithName() using name "Lucida Grande" and got
font with PostScript name "LucidaGrande". For best performance, only use
PostScript names when calling this API.>



5 minutes with Google suggests this is a harmless warning message issued 
by the library on the Mac that handles fonts.


As for the missing plot window, have you tried following Jeff's advice 
to George from over the weekend?


B


--
 Bruce Ravel   bra...@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
___
Ifeffit mailing list
Ifeffit@millenia.cars.aps.anl.gov
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit