Re: about atoms.inp data of As2O3 (arsenious oxide)
On Monday 08 May 2006 08:47, you wrote:
I am a Ph.D. student in Gwangju Institute Science and Technology, South Korea. I have been tried to analyze my EXAFS sample with reference of As2O3 (arsenious oxide) obtained from "The Atoms.inp Archive (http://cars9.uchicago.edu/~newville/adb/search.html). But I could not run the feff in the Artemis (version 0.8.006) successfully with the As2O3 atoms file. Could you let me know how to solve the problem? It would be very honor to me if you let suggest a clue for the problem, sir.
Ji-Hoon, This is the sort of question that should be asked on the Ifeffit mailing list, so I am taking the liberty of CCing my answer there. I agree that the input file for As2O3 from the database is wrong. It generates an obviously incorrect list of coordinates. You need to go to the crystallography literature and find the correct data for that structure. There is nothing wrong (at least with respect to this question!) with Artemis. It seems likely that the problem is with the reliability of the data for As2O3 in the database. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/
Mincryst has two crystal forms of As2O3. One of these is claudetite, for
which they give the following data:
1, t-claudetite, form I, f-arsenolite
As(2)O(3)
Monoclinic P 2(1)/n Z = 4
F.Pertlik (1978)
* Mh. Chem., 109, 277-282
Lattice parameters (cub. angs.,degr.):
a = 5.2500 alpha = 90.00
b = 12.9900 beta = 93.88
c = 4.5300 gamma = 90.00
Co-ordinates, thermal parameters, occupation for atomic positions:
NoP x/a y/b z/c B(j) atom / occupation
1 0.2577 0.1017 0.0423 0.00 As = 1.00
2 0.3584 0.3504 0.0043 0.00 As = 1.00
3 0.4353 0.2190 0.0624 0.00 O = 1.00
4 0.6613 0.3975 0.1513 0.00 O = 1.00
5 0.9608 0.1381 0.1452 0.00 O = 1.00
Full unit cell contains 20 positions
X-ray density (g/cm cub.) = 4.26
and the other is arsenolite:
Cubic F d3m Z = 16
Ref.Str.:
Pertlik F. (1978)
* Czech. J. Phys., B28, 170-176
Lattice parameters (cub. angs.,degr.):
a = 11.0740 alpha = 90.00
b = 11.0740 beta = 90.00
c = 11.0740 gamma = 90.00
Co-ordinates, thermal parameters, occupation for atomic positions:
NoP x/a y/b z/c B(j) atom / occupation
1 0.8971 0.8971 0.8971 0.00 As = 1.00
2 0.1726 0.0000 0.0000 0.00 O = 1.00
Full unit cell contains 80 positions
X-ray density (g/cm cub.) = 3.87
I don't know which is the more common form or more likely. Both yield
3-coordinate As.
mam
----- Original Message -----
From: "Bruce Ravel"
On Monday 08 May 2006 08:47, you wrote:
I am a Ph.D. student in Gwangju Institute Science and Technology, South Korea. I have been tried to analyze my EXAFS sample with reference of As2O3 (arsenious oxide) obtained from "The Atoms.inp Archive (http://cars9.uchicago.edu/~newville/adb/search.html). But I could not run the feff in the Artemis (version 0.8.006) successfully with the As2O3 atoms file. Could you let me know how to solve the problem? It would be very honor to me if you let suggest a clue for the problem, sir.
Ji-Hoon,
This is the sort of question that should be asked on the Ifeffit mailing list, so I am taking the liberty of CCing my answer there.
I agree that the input file for As2O3 from the database is wrong. It generates an obviously incorrect list of coordinates. You need to go to the crystallography literature and find the correct data for that structure.
There is nothing wrong (at least with respect to this question!) with Artemis. It seems likely that the problem is with the reliability of the data for As2O3 in the database.
B
-- Bruce Ravel ---------------------------------------------- bravel@anl.gov
Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007
Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793
My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
On Monday 08 May 2006 11:36, you wrote:
Mincryst has two crystal forms of As2O3. One of these is claudetite, for which they give the following data: 1, t-claudetite, form I, f-arsenolite
Oooh! That's cool. I had never seen that database before. I just made an Ifeffit FAQ entry for links to crystal structure databases. It's the second item at http://cars9.uchicago.edu/iffwiki/FAQ/RunningFeff If you know of any more good ones, feel free to add to the FAQ entry. B -- Bruce Ravel ---------------------------------------------- bravel@anl.gov Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007 Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793 My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/
Also the Crystallography Open Database http://www.crystallography.net (I added it to the wiki already Bruce!) Carlo On Mon, 8 May 2006, Bruce Ravel wrote:
On Monday 08 May 2006 11:36, you wrote:
Mincryst has two crystal forms of As2O3. One of these is claudetite, for which they give the following data: 1, t-claudetite, form I, f-arsenolite
Oooh! That's cool. I had never seen that database before. I just made an Ifeffit FAQ entry for links to crystal structure databases. It's the second item at
http://cars9.uchicago.edu/iffwiki/FAQ/RunningFeff
If you know of any more good ones, feel free to add to the FAQ entry.
B
-- 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 Carlo.Segre@iit.edu http://www.iit.edu/~segre
It's a mineralogy database. I've found an error in it, so I know it's not
perfect.
The URL for the search screen is
http://database.iem.ac.ru/mincryst/search.php? .
The ? is part of the URL, even though my mailer doesn't seem to think it
should be.
mam
----- Original Message -----
From: "Bruce Ravel"
On Monday 08 May 2006 11:36, you wrote:
Mincryst has two crystal forms of As2O3. One of these is claudetite, for which they give the following data: 1, t-claudetite, form I, f-arsenolite
Oooh! That's cool. I had never seen that database before. I just made an Ifeffit FAQ entry for links to crystal structure databases. It's the second item at
http://cars9.uchicago.edu/iffwiki/FAQ/RunningFeff
If you know of any more good ones, feel free to add to the FAQ entry.
B
-- Bruce Ravel ---------------------------------------------- bravel@anl.gov
Molecular Environmental Science Group, Building 203, Room E-165 MRCAT, Sector 10, Advanced Photon Source, Building 433, Room B007
Argonne National Laboratory phone and voice mail: (1) 630 252 5033 Argonne IL 60439, USA fax: (1) 630 252 9793
My homepage: http://cars9.uchicago.edu/~ravel EXAFS software: http://cars9.uchicago.edu/~ravel/software/
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Bruce Ravel wrote:
Ifeffit FAQ entry for links to crystal structure databases. It's the second item at
http://cars9.uchicago.edu/iffwiki/FAQ/RunningFeff
If you know of any more good ones, feel free to add to the FAQ entry.
I added the ICSD at ILL:
http://icsd.ill.fr
M.
--
Mauro Rovezzi
participants (5)
-
Bruce Ravel
-
Carlo Segre
-
Matthew
-
Matthew Marcus
-
Mauro Rovezzi