[Ifeffit] about wolframite crystallographic file (Ravel, Bruce)

Yordy Licea Fonseca yliceafonseca at gmail.com
Tue Nov 25 19:45:52 CST 2008


Hi all,

In my case, Artemis version 0.8.012 (c), the error in Echo is just:
"Artemis trapped one or more errors!  Error message dumped to screen."
Thank you very much, the problem is solved the way Dominik and Carl have
suggested.

Best regards,
Yordy



2008/11/17 <ifeffit-request at millenia.cars.aps.anl.gov>

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> Today's Topics:
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>   1. Re: about wolframite crystallographic file (Ravel, Bruce)
>   2. Re: about wolframite crystallographic file (Dominik Samuelis)
>   3. Re: about wolframite crystallographic file (Ponader, Carl W Dr)
>   4. Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on
>      Ubuntu from source (Mauro Rovezzi)
>   5. Re: [PGPLOT build problem] Upgrading to ifeffit-1.2.11b on
>      Ubuntu from source (Carlo Segre)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 17 Nov 2008 09:16:25 -0500
> From: "Ravel, Bruce" <bravel at bnl.gov>
> Subject: Re: [Ifeffit] about wolframite crystallographic file
> To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <8FA2653072F45348BC6E32FEB95CDC62D3D1 at exchangemb5.bnl.gov>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Yordy,
>
> I'll look into this when I get a chance, but that might not be until later
> in the week (I am on travel at the moment).
>
> B
>
> --
>  Bruce Ravel  ----------------------------------- bravel at bnl.gov
>
>  National Institute of Standards and Technology
>  Synchrotron Methods Group at Brookhaven National Laboratory
>  Building 535A
>  Upton NY, 11973
>
>  My homepage:    http://cars9.uchicago.edu/~ravel
>  EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>
>
>
>
> -----Original Message-----
> From: ifeffit-bounces at millenia.cars.aps.anl.gov on behalf of Yordy Licea
> Fonseca
> Sent: Sat 11/15/2008 6:36 PM
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] about wolframite crystallographic file
>
> Hi all,
>
> As soon as I load this attached CIF crystallographic file from ISCD in
> Artemis0.8.012 the software says:
> "Artemis trapped one or more errors!  Error message dumped to screen."
> I can`t go on runnig Atoms as it seems to be a problem with the file. I
> have
> read the suggestion made in FAQ, but I can not manage to find the error.
> Could you help me, please?
> It would be nice once the problem been fixed to add this structure to
> Matt's
> atoms.inp database.
>
> Thanks you very much, Yordy
>
> --
> Yordy E. Licea Fonseca
> Departamento de F?sico-Qu?mica
> Instituto de Qu?mica-IQ/UFRJ
> Laborat?rio de Cat?lise Heterog?nea
> Rio de Janeiro, RJ, CEP 21.949-909
> Brasil
> Email: yliceafonseca at gmail.com
>
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> ------------------------------
>
> Message: 2
> Date: Mon, 17 Nov 2008 16:04:15 +0100
> From: Dominik Samuelis <d.samuelis at fkf.mpg.de>
> Subject: Re: [Ifeffit] about wolframite crystallographic file
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <492187EF.4010708 at fkf.mpg.de>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Dear Yordy,
>
> this error message actually occured because the crystallographic data in
> the .cif file is somewhat ambigous. The space group is P 2/c (number
> 13), which is a monoclinic cell (with two different settings, as
> additional complication: unique axis b or c).
>
> Now, if you look in the .cif file, the unit cell parameters are given as
> follows:
>
> -- snip
> _cell_length_a                     4.6698(9)
> _cell_length_b                     5.6873(23)
> _cell_length_c                     4.9515(17)
> _cell_angle_alpha                  90.
> _cell_angle_beta                   90.(0)
> _cell_angle_gamma                  90.
> -- snip
>
> You can see, that in the cif file, all angles are 90.0000 degrees. This
> however would be an orthorhombic cell, not a monoclinic. That's exactly
> the contents of the Artemis/Atoms error message:
>
> "Monoclinic cells have all unequal axes and one non-right angle.
> Unknown setting for a monoclinic cell.
>
> Fatal error(s) in cell parameters."
>
> The atoms code in this case is not able to determine the setting of the
> monoclinic cell, because it cannot find the unique axis. For humans, the
> unique axis is denoted by the standard deviation (0) behind beta, making
> it unique axis b. This however is not interpreted by Artemis.
>
> This means, that you have to tell Artemis in some way, which angle
> deviates from 90?. For this, I usually change the beta angle in the cif
> file by some tiny amount, to -say- 90.0001 degrees. This is far below
> the standard deviation, so it's crystallographically still valid.
>
> -- snip
> _cell_angle_alpha                  90.
> _cell_angle_beta                   90.0001(0)
> _cell_angle_gamma                  90.
> -- snip
>
>
> Cheers,
> dominik
>
> Yordy Licea Fonseca wrote:
> > Hi all,
> >
> > As soon as I load this attached CIF crystallographic file from ISCD in
> > Artemis0.8.012 the software says:
> > "Artemis trapped one or more errors!  Error message dumped to screen."
> > I can`t go on runnig Atoms as it seems to be a problem with the file. I
> > have read the suggestion made in FAQ, but I can not manage to find the
> > error.
> > Could you help me, please?
> > It would be nice once the problem been fixed to add this structure to
> > Matt's atoms.inp database.
> >
> > Thanks you very much, Yordy
> >
> > --
> > Yordy E. Licea Fonseca
> > Departamento de F?sico-Qu?mica
> > Instituto de Qu?mica-IQ/UFRJ
> > Laborat?rio de Cat?lise Heterog?nea
> > Rio de Janeiro, RJ, CEP 21.949-909
> > Brasil
> > Email: yliceafonseca at gmail.com <mailto:yliceafonseca at gmail.com>
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > Ifeffit mailing list
> > Ifeffit at millenia.cars.aps.anl.gov
> > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> --
> Dr. Dominik Samuelis
> d.samuelis at fkf.mpg.de
> Max-Planck-Institut f?r Festk?rperforschung
> Max Planck Institute for Solid State Research
> Heisenbergstr. 1
> 70569 Stuttgart
> Germany
> Phone +49-711-689-1769
> Fax   +49-711-689-1722
> Web   http://www.fkf.mpg.de/maier/
>
>
>
> ------------------------------
>
> Message: 3
> Date: Mon, 17 Nov 2008 09:49:50 -0500
> From: "Ponader, Carl W Dr" <PonaderCW at corning.com>
> Subject: Re: [Ifeffit] about wolframite crystallographic file
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID:
>        <EEA3BD28F7457C4A94CFB4048FA27EE949068E at cvcv0xi04.na.corning.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Yordy, Bruce
>
>
>
> Apparently Atoms doesn't like it that the beta angle in a monoclinic cell
> is 90 degrees.  When I change the beta angle to 91 degrees or even 90.0001
> (and change nothing else), Atoms runs normally.  It's interesting that
> although Artemis says it has written a message nothing shows up in the
> messages palette but the echo palette does show that an error was caught.
>
>
>
> Carl
>
>
>
> ________________________________
>
> From: ifeffit-bounces at millenia.cars.aps.anl.gov [mailto:
> ifeffit-bounces at millenia.cars.aps.anl.gov] On Behalf Of Yordy Licea
> Fonseca
> Sent: Saturday, November 15, 2008 6:36 PM
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] about wolframite crystallographic file
>
>
>
> Hi all,
>
>
>
> As soon as I load this attached CIF crystallographic file from ISCD in
> Artemis0.8.012 the software says:
>
> "Artemis trapped one or more errors!  Error message dumped to screen."
>
> I can`t go on runnig Atoms as it seems to be a problem with the file. I
> have read the suggestion made in FAQ, but I can not manage to find the
> error.
>
> Could you help me, please?
>
> It would be nice once the problem been fixed to add this structure to
> Matt's atoms.inp database.
>
>
>
> Thanks you very much, Yordy
>
> --
> Yordy E. Licea Fonseca
> Departamento de F?sico-Qu?mica
> Instituto de Qu?mica-IQ/UFRJ
> Laborat?rio de Cat?lise Heterog?nea
> Rio de Janeiro, RJ, CEP 21.949-909
> Brasil
> Email: yliceafonseca at gmail.com
>
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> ------------------------------
>
> Message: 4
> Date: Mon, 17 Nov 2008 17:07:39 +0100
> From: Mauro Rovezzi <rovezzi at esrf.fr>
> Subject: Re: [Ifeffit] [PGPLOT build problem] Upgrading to
>        ifeffit-1.2.11b on Ubuntu from source
> To: segre at agni.phys.iit.edu,    XAFS Analysis using Ifeffit
>        <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <492196CB.3000200 at esrf.fr>
> Content-Type: text/plain; charset=windows-1252; format=flowed
>
> Carlo Segre wrote:
> >
> > Hi Mauro:
> >
> > I have now produced a package of ifeffit 1.2.11b.  It is in Debian
> > unstable and available for Ubuntu intrepid and jaunty in my repository
> >
> > deb http://debian-xray.iit.edu intrepid main contrib non-free
>
> Carlo,
>
> Thank you very much for the package.
>
> Actually, I was able to build/install ifeffit 1.2.11b from source but
> not able to build than the Perl/Python wrappers and so no Horae&Friends
> from Bruce SVN.
>
> Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and
> "python-ifeffit" from binaries and "libperlxray" "horae" and "demeter"
> built from source (Bruce SVN).
>
> Everything seems fine but I still do not understand why ifeffit 1.2.11
> has all these "IFF str = *" output as stated also by Gareth in his
> "Ifeffit 1.2.11b terminal output" post. Is it normal?
>
> Cheers,
> Mauro
>
>
> ------------------------------
>
> Message: 5
> Date: Mon, 17 Nov 2008 11:32:37 -0600 (CST)
> From: Carlo Segre <segre at iit.edu>
> Subject: Re: [Ifeffit] [PGPLOT build problem] Upgrading to
>        ifeffit-1.2.11b on Ubuntu from source
> To: Mauro Rovezzi <rovezzi at esrf.fr>
> Cc: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Message-ID: <alpine.DEB.2.00.0811171039320.3650 at hydride.iit.edu>
> Content-Type: text/plain; charset=us-ascii; format=flowed
>
>
> Hi Mauro:
>
> On Mon, 17 Nov 2008, Mauro Rovezzi wrote:
>
> > Carlo Segre wrote:
> >>
> >> I have now produced a package of ifeffit 1.2.11b.  It is in Debian
> unstable
> >> and available for Ubuntu intrepid and jaunty in my repository
> >>
> >> deb http://debian-xray.iit.edu intrepid main contrib non-free
> >
> > Thank you very much for the package.
> >
> > Actually, I was able to build/install ifeffit 1.2.11b from source but not
> > able to build than the Perl/Python wrappers and so no Horae&Friends from
> > Bruce SVN.
> >
> > Well, now I have "pgplot5", "ifeffit", "perl-ifeffit" and
> "python-ifeffit"
> > from binaries and "libperlxray" "horae" and "demeter" built from source
> > (Bruce SVN).
> >
>
> yeah, I have not completed packaging the new horae.  Because of the way
> Bruce has restructured it, I have had to package several new perl modules
> and change the build system on the horae programs.  I ust need to spend a
> bit more time on it to get it it right.  maybe next weekend :-)
>
> > Everything seems fine but I still do not understand why ifeffit 1.2.11
> has
> > all these "IFF str = *" output as stated also by Gareth in his "Ifeffit
> > 1.2.11b terminal output" post. Is it normal?
> >
>
> I don't know why this is happening but it looks to me simply like a dump
> of the ifeffit commands which are being executed.  It is annoying but I
> haven't seen any problems because of it.
>
> Carlo
>
> --
> Carlo U. Segre -- Professor of Physics
> Associate Dean for Special Projects, Graduate College
> Illinois Institute of Technology
> Voice: 312.567.3498            Fax: 312.567.3494
> segre at iit.edu   http://www.iit.edu/~segre   segre at debian.org
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
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>
> End of Ifeffit Digest, Vol 69, Issue 12
> ***************************************
>



-- 
Yordy E. Licea Fonseca
Departamento de Físico-Química
Instituto de Química-IQ/UFRJ
Laboratório de Catálise Heterogênea
Rio de Janeiro, RJ, CEP 21.949-909
Brasil
Email: yliceafonseca at gmail.com
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