[Ifeffit] Demeter-devel MacPorts Athena issues & work-around

Mon Jul 7 09:51:32 CDT 2014

Bruce,
I understand that it is frustrating to try to help someone when you are
given only part of the information needed to fully solve a problem. I'm
sure it is an issue you deal with on a relatively regular basis. I do want
to particularly thank you, though, for quickly fixing both of my problems
-- especially over the 4th of July weekend. I did not expect such a quick
response -- it was a great help to have Athena working like she usually
does this weekend.

With regard to your discussion with Matt about the underlying issue
hindering the opening of these files into Athena, I would like to mention
that these data files load in just fine to Athena using Demeter on a
Windows operating system and with the iXAFS program version 2.2 for Intel
Macs. I'm not sure if that helps, or is even relevant, but I thought I
would let you know.

Again, thank you for all your help.

Best regards,
Margaret Anne

------------------------------------
Margaret Anne G. Hinkle
Ph.D. Candidate
Earth and Planetary Sciences
Washington University in St. Louis
Rudolph Hall
Campus Box 1169
1 Brookings Drive
St. Louis, MO 63130
email: mhinkle at eps.wustl.edu
website: aqgeochem.wustl.edu

On Sun, Jul 6, 2014 at 5:24 PM, Bruce Ravel <bravel at bnl.gov> wrote:

>
> Matt,
>
> You're right.  I was too grouchy.  Margaret Anne, I apologize if I was too
> mean-spirited in my emails over the weekend.
>
>
>
> On 07/06/2014 05:54 PM, Matt Newville wrote:
>
>> Wait, what?   What text string is configured to be only 256 characters?
>> Something must be very wrong with the Macports installation - this file
>> opens just fine for me, though I haven't tested it with the Macports
>> version.
>>
>> The "read_data()" command in ifeffit uses a line length of 2048
>> characters, and should not crash on a longer line, but truncate lines to
>> 2048 characters (silently, which is irritating when encountered, but not
>> as bad as crashing).     I've written and used thousands of data files
>> with comment and data lines longer than 256 characters.    I believe
>> there is (and should be) nothing in the code for reading data that sets
>> a limit as low as 256 characters (File names are allowed to be 512
>> characters!), and nothing that should cause a crash on larger lines.
>>
>> Of course it's fine to use a plugin for specific file types, and
>> probably wise to not rely of ifeffit's read_data() for really big files
>> (though, again, I regularly read files of 35 to 40 columns without a
>> plugin).   But this seems to me like its a Macports-only problem to me
>> that should be fixed.
>>
>
> I guess I explained it poorly, but it is not a MacPorts-only problem.
>
> It /opens/ just fine.  That's not the problem.
>
> It's a problem with iff_show, which Athena uses to fetch the names of the
> column labels after ifeffit reads the data file.  Here's what happens if
> you exercise iff_show by hand:
>
> bruce at atropos [demeter] > ifeffit
>  Ifeffit  1.2.11d Copyright (c) 2008 Matt Newville, Univ of Chicago
>                 command-line shell version 1.1 with GNU Readline
> Ifeffit> read_data (file="/home/bruce/Mn0214_7dMnO2_Header_exafsscan1.dat",
> group=a)
> Ifeffit> show @strings
>  $plot_devices  = /png /tpng /null /ps /vps /cps /vcps /xwindow /xserve
>  $plot_device   = /xserve
>  $group         = a
>  $commentchar   = #
>  $&build        = 1.2.11d Copyright (c) 2008 Matt Newville, Univ of Chicago
>  $&install_dir  = /usr/local/share/ifeffit
>  $column_label  = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
> 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47
> 48 49 50 51 52 53 54 55 56 57
>  $column_label1 = 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
> 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47
> 48 49 50 51 52 53 54 55 56 57
>  $a_title_01    = S 1  exafsscan
>  $a_title_02    = C exafs_edge_energy 6.539
>  $a_title_03    = C exafs_region -150 -20 26 1 0 0 0
>  $a_title_04    = C exafs_region -20 34.1959 108 1 0 0 0
>  $a_title_05    = C exafs_region 34.1959 972.683 260 1 0 1 1.4
>  $a_title_06    = D Wed Feb 26 22:19:02 2014
>  $a_title_07    = T 4.58834  (Seconds)
>  $a_title_08    = G0 0
>  $a_title_09    = G1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
> 0 0 0 0 0
>  $a_title_10    = G3 0 0 0 0 0 0 0 0 0
>  $a_title_11    = G4 0
>  $a_title_12    = Q
>  $a_title_13    = P0 17.707645 -0.3425 33.862069 -0.80317213 -18.366667
> 0.175013 -0.175013 8.99922
>  $a_title_14    = P1 8.49884 8.74903 -5.0037582 8.74903 1.7763568e-14 0
> 3.5002457 9.4148
>  $a_title_15    = P2 -44.9992 -23.95 -30.75 97.52 19.252 -11.58 8.4175
> -2.25125
>  $a_title_16    = P3 -5.11125 1.4875 0.7325 1.5 85 0 -600
>  $a_title_17    = N 57
>
> At line 436 of file iff_show.f
> Fortran runtime error: End of record
> bruce at atropos [demeter] >
>
>
> Line 436 of iff_show is
>
>        write(messg,11)  s(1:k), ' = ', t(1:j)
>
> messg is defined just above that as character*256.  I interpreted this as
> attempting to put a 330 character string in a character*256 variable.  But,
> in truth, I did not examine the code all that closely.
>
> I suppose I could have worked on fixing Ifeffit, but the plugin took way
> less time.  And my time would be better spent making Demeter use Larch
> properly.
>
>
> B
>
>
>
> --
>  Bruce Ravel  ------------------------------------ bravel at 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
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>
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