Re: [Ifeffit] problems installing athena et al under ubuntu 16.04 LTS

2016-12-02 Thread Juan de la figuera 
Just tested it. Great!

Juan

El jue., 1 dic. 2016 a las 22:58, Bruce Ravel () escribió:

> I just checked a fix into github that addresses the problem Juan
> identified.  Matt's assessment at
> https://github.com/bruceravel/demeter/issues/42 was exactly right.  I
> adopted his second solution.
>
> Thanks to all of you for this discussion.
> B
>
>
>
> On 11/25/2016 05:23 AM, Juan de la figuera wrote:
> > Hi,
> >
> > I send one of the data files we are currently acquiring (SPLINE beamline
> > at ESRF).
> >
> > I have checked that my compiled 0.9.24 version works with the examples
> > cu10k.dat file, but it is true, as Robert confirmed, that strange things
> > happen if you mark ev instead of kev.
> >
> > With our data files like the one enclosed, dathena chokes on the scale.
> > Actually it opens the window but it has x10^9 scale. On the other hand,
> > the 0.9.24 for Windows opens the files ok. Now, the files are
> > MSDOS-ended files, I tried converting them to Linux-ending, but same
> > result. I also tried putting a # comment on the first line.
> >
> > I stress that Athena 0.8.061 (included in the horae package in ubuntu)
> > opens the file like a charm.
> >
> > One additional detail (just in case), I have Ubuntu 16.04 LTS 64-bit.
> >
> > Best,
> > Juan
> >
> >
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>
>
> --
>   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] error message when trying to reopen Artemis file

2016-12-02 Thread Bruce Ravel 

On 12/02/2016 09:01 AM, Bruce Ravel wrote:


Your cif file triggered a very specific bug in my software that has
nothing to do with your recent difficulties.

Had you picked almost any other cif file for any other material, you
would have been fine.

I am guessing you chose this one:

  http://www.crystallography.net/cod/cod/cif/7/20/60/7206075.cif

or something very similar.  Demeter makes a mistake parsing the space
group symbol in that file.

Try this:

  http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp

It seems to work correctly without triggering the specific problem that
the cif file triggers which, again, has to do with the specific symbol
used and how Demeter parses it.


Thanks for reporting this.  I'll work on it.



I just pushed a fix for this to github.

The project file you sent me is not fixable (well ... not easily).  The 
best thing to do is to discard it and start again.


Thanks again for uncovering a fairly obscure bug!

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] error message when trying to reopen Artemis file

2016-12-02 Thread Bruce Ravel 


Marcus,

Your cif file triggered a very specific bug in my software that has 
nothing to do with your recent difficulties.


Had you picked almost any other cif file for any other material, you 
would have been fine.


I am guessing you chose this one:

  http://www.crystallography.net/cod/cod/cif/7/20/60/7206075.cif

or something very similar.  Demeter makes a mistake parsing the space 
group symbol in that file.


Try this:

  http://cars9.uchicago.edu/atomsdb/TiO2-ana.inp

It seems to work correctly without triggering the specific problem that 
the cif file triggers which, again, has to do with the specific symbol 
used and how Demeter parses it.



Thanks for reporting this.  I'll work on it.

B

On 12/02/2016 06:07 AM, mfehse wrote:

Hi

so i have created a little Artemis project to practice. Its tio2 data
file with anatase cif file, i just included teh first path but havent
done any fitting yet. When i close artemis and want to reopen it I get
the following error:

"You must define a method name at
/usr/lib/i386-linux-gnu/perl5/5.22/Class/MOP/Mixin/HasMethods.pm line 96

Class::MOP::Mixin::HasMethods::has_method('Class::MOP::Class::Immutable::Moose::Meta::Class::__ANON__::SERIAL::1=HASH(0xe06c454)',
'') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 442
Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x106b5394)', ' :')
called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 465
Demeter::Atoms::parse_line('Demeter::Atoms=HASH(0x106b5394)', 'space
= I 41/a m d :1') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 390
Demeter::Atoms::read_inp('Demeter::Atoms=HASH(0x106b5394)') called
at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 200
Demeter::Atoms::__ANON__('Demeter::Atoms=HASH(0x106b5394)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp', '')
called at accessor Demeter::Atoms::file (defined at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/Atoms.pm
line 204) line 10
Demeter::Atoms::file('Demeter::Atoms=HASH(0x106b5394)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp')
called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Atoms/Xtal.pm
line 667

Demeter::UI::Atoms::Xtal::open_file('Demeter::UI::Atoms::Xtal=HASH(0x1312b8e0)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp')
called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm
line 1388
Demeter::UI::Artemis::make_feff_frame('Wx::Frame=HASH(0x127f5b3c)',
'/home/marquinhos/.horae/stash/_dem_djyzliqy/feff/gflkw/atoms.inp',
1010942) called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis/Project.pm
line 351
Demeter::UI::Artemis::Project::read_project('HASH(0x102e8084)',
'/home/marquinhos/Desktop/TIO2_tryout.fpj') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm
line 1026
Demeter::UI::Artemis::OnMenuClick('Wx::Frame=HASH(0x127f5b3c)',
'Wx::CommandEvent=SCALAR(0x12ab14cc)') called at
/home/marquinhos/perl5/lib/perl5/i686-linux-gnu-thread-multi-64int/Demeter/UI/Artemis.pm
line 440
Demeter::UI::Artemis::__ANON__('Wx::Frame=HASH(0x127f5b3c)',
'Wx::CommandEvent=SCALAR(0x12ab14cc)') called at demeter/bin/dartemis
line 31
eval {...} at demeter/bin/dartemis line 31
"

i have attached the project so you can try if you can open it on your
artemis

many thanks

marcus

On 01/12/2016 19:26, Bruce Ravel wrote:

On 12/01/2016 01:20 PM, mfehse wrote:


and am now able to launch the athena and it seems to work, however i
still get the error message:
"Could not find Larch Server -- falling back to Ifeffit"
is this something i should care about?


Nope.

It's a message that will eventually go away.  Right now, Matt and I
are working on migrating to Larch.  This week we have been figuring
out how to make Athena's interaction with Larch work reliably.  That
message is there so that I know what is going on while I am working on
the code. In this case, it is Demeter telling you that it is
gracefully recognizing that you do not have Larch installed.

If you don't want to be looking at the head of the main branch, then
you could download the zip file for the most recently tagged release:
https://github.com/bruceravel/demeter/tree/0.9.25

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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