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

Send Ifeffit mailing list submissions to
ifeffit@millenia.cars.aps.anl.gov

To subscribe or unsubscribe via the World Wide Web, visit
http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
or, via email, send a message with subject or body 'help' to
ifeffit-request@millenia.cars.aps.anl.gov

You can reach the person managing the list at
ifeffit-owner@millenia.cars.aps.anl.gov

When replying, please edit your Subject line so it is more specific
than "Re: Contents of Ifeffit digest..."

Today's Topics:

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@bnl.gov>
Subject: Re: [Ifeffit] about wolframite crystallographic file
To: "XAFS Analysis using Ifeffit" <ifeffit@millenia.cars.aps.anl.gov>
Message-ID: <8FA2653072F45348BC6E32FEB95CDC62D3D1@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@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@millenia.cars.aps.anl.gov on behalf of Yordy Licea Fonseca
Sent: Sat 11/15/2008 6:36 PM
To: ifeffit@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@gmail.com

-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: application/ms-tnef
Size: 3525 bytes
Desc: not available
Url : http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20081117/0638d889/attachment-0001.bin

------------------------------

Message: 2
Date: Mon, 17 Nov 2008 16:04:15 +0100
From: Dominik Samuelis <d.samuelis@fkf.mpg.de>
Subject: Re: [Ifeffit] about wolframite crystallographic file
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Message-ID: <492187EF.4010708@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@gmail.com <mailto:yliceafonseca@gmail.com>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit@millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit

--
Dr. Dominik Samuelis
d.samuelis@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@corning.com>
Subject: Re: [Ifeffit] about wolframite crystallographic file
To: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Message-ID:
<EEA3BD28F7457C4A94CFB4048FA27EE949068E@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@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Yordy Licea Fonseca
Sent: Saturday, November 15, 2008 6:36 PM
To: ifeffit@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@gmail.com

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20081117/2a963a23/attachment-0001.html

------------------------------

Message: 4
Date: Mon, 17 Nov 2008 17:07:39 +0100
From: Mauro Rovezzi <rovezzi@esrf.fr>
Subject: Re: [Ifeffit] [PGPLOT build problem] Upgrading to
ifeffit-1.2.11b on Ubuntu from source
To: segre@agni.phys.iit.edu, XAFS Analysis using Ifeffit
<ifeffit@millenia.cars.aps.anl.gov>
Message-ID: <492196CB.3000200@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@iit.edu>
Subject: Re: [Ifeffit] [PGPLOT build problem] Upgrading to
ifeffit-1.2.11b on Ubuntu from source
To: Mauro Rovezzi <rovezzi@esrf.fr>
Cc: XAFS Analysis using Ifeffit <ifeffit@millenia.cars.aps.anl.gov>
Message-ID: <alpine.DEB.2.00.0811171039320.3650@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@iit.edu http://www.iit.edu/~segre segre@debian.org

------------------------------

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

End of Ifeffit Digest, Vol 69, Issue 12
***************************************