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

[Yordy Licea Fonseca]

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 <[EMAIL PROTECTED]>

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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)
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>
> ----------
>
> Message: 1
> Date: Mon, 17 Nov 2008 09:16:25 -0500
> From: "Ravel, Bruce" <[EMAIL PROTECTED]>
> Subject: Re: [Ifeffit] about wolframite crystallographic file
> To: "XAFS Analysis using Ifeffit" 
> Message-ID: <[EMAIL PROTECTED]>
> 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  --- [EMAIL PROTECTED]
>
>  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: [EMAIL PROTECTED] 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: [EMAIL PROTECTED]
>
> -- next part --
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> --
>
> Message: 2
> Date: Mon, 17 Nov 2008 16:04:15 +0100
> From: Dominik Samuelis <[EMAIL PROTECTED]>
> Subject: Re: [Ifeffit] about wolframite crystallographic file
> To: XAFS Analysis using Ifeffit 
> Message-ID: <[EMAIL PROTECTED]>
> 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. degrees. This
> however would be an orthorhombic cell, not a monoclinic. That's exactly
> the contents of the Artemis

Re: [Ifeffit] about wolframite crystallographic file

[Ponader, Carl W Dr]

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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] 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 Físico-Química 
Instituto de Química-IQ/UFRJ 
Laboratório de Catálise Heterogênea 
Rio de Janeiro, RJ, CEP 21.949-909 
Brasil 
Email: [EMAIL PROTECTED]

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Re: [Ifeffit] about wolframite crystallographic file

[Dominik Samuelis]

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. 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 Físico-Química
> Instituto de Química-IQ/UFRJ
> Laboratório de Catálise Heterogênea
> Rio de Janeiro, RJ, CEP 21.949-909
> Brasil
> Email: [EMAIL PROTECTED] 
> 
> 
> 
> 
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-- 
Dr. Dominik Samuelis
[EMAIL PROTECTED]
Max-Planck-Institut für Festkörperforschung
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/

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Re: [Ifeffit] about wolframite crystallographic file

[Ravel, Bruce]

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  --- [EMAIL PROTECTED]

 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: [EMAIL PROTECTED] 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 Físico-Química
Instituto de Química-IQ/UFRJ
Laboratório de Catálise Heterogênea
Rio de Janeiro, RJ, CEP 21.949-909
Brasil
Email: [EMAIL PROTECTED]

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