On Sunday 06 January 2008 11:26:53 you wrote:
Is there a way to calculate or read feff7 or FEFF8 paths with the last version of Artemis? I could not find this information on this page:
http://cars9.uchicago.edu/~ravel/software/aboutartemis.html
and this option is not listed in your to-do list. I suppose that there is a good reason for it!
Implementing the possibility to read at once several FEFF paths (for example from the list.dat file) could be useful, I think.
Alain, I am CCing this general interest question to the mailing list. Artemis does not actually have a preference for the version of feff that you use. Since Feff is run as an external process, all you need to do is configure Artemis to use your prefered version. * In the Edit menu, select "Edit preferences". * In the Atoms groups, change `template' to "feff7" or "feff8", as you wish. That will have the effect of changing what kind of feff.inp file atoms makes. * In the Feff group, change `feff_executable' to the version of feff you are using. If the executable is not in the execution path, you will need to enter the fully resolved path as the value for that configuration parameter. If you have run feff independently of Artemis and simply wish to import the feffNNNN.dat files, that should work with no regard to the version of Feff that you used. The format of the feffNNNN.dat file did not change between feff6 and feff8. If you are seeing some particular failure of Artemis, then you will need to show me what happens. Without providing enough information for me to reproduce the problem on my own computer, it is not reasonable to expect that I can solve a problem. HTH, B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Bruce, Thank you for the clarification. I progressed, but still encounter a problem running FEFF7. The error message and the input parameters and configuration are shown in the ppt in attachment. Thanks Alain At 14:58 07/01/2008, you wrote:
On Sunday 06 January 2008 11:26:53 you wrote:
Is there a way to calculate or read feff7 or FEFF8 paths with the last version of Artemis? I could not find this information on this page:
http://cars9.uchicago.edu/~ravel/software/aboutartemis.html
and this option is not listed in your to-do list. I suppose that there is a good reason for it!
Implementing the possibility to read at once several FEFF paths (for example from the list.dat file) could be useful, I think.
Alain,
I am CCing this general interest question to the mailing list.
Artemis does not actually have a preference for the version of feff that you use. Since Feff is run as an external process, all you need to do is configure Artemis to use your prefered version.
* In the Edit menu, select "Edit preferences".
* In the Atoms groups, change `template' to "feff7" or "feff8", as you wish. That will have the effect of changing what kind of feff.inp file atoms makes.
* In the Feff group, change `feff_executable' to the version of feff you are using. If the executable is not in the execution path, you will need to enter the fully resolved path as the value for that configuration parameter.
If you have run feff independently of Artemis and simply wish to import the feffNNNN.dat files, that should work with no regard to the version of Feff that you used. The format of the feffNNNN.dat file did not change between feff6 and feff8.
If you are seeing some particular failure of Artemis, then you will need to show me what happens. Without providing enough information for me to reproduce the problem on my own computer, it is not reasonable to expect that I can solve a problem.
HTH, B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973
My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Alain, I had a similar problem trying to run FEFF8.2 in Artemis on my WinXP machine. The simple fix is to have a folder outside Artemis where you "store" the FEFF executable and an input file. FEFF will write the feffnnnn.dat files to that folder. Then, import the input file into Artemis, as long as the feffnnnn.dat files are in the same folder as the input file, it will work. I can't help you with your other question regarding why the plots don't reflect your fit parameters. It might help others though if you send the project file to look at. For those who don't have access to PowerPoint, a pdf of Alain's ppt is attached. Richard
Bruce,
Thank you for the clarification. I progressed, but still encounter a problem running FEFF7. The error message and the input parameters and configuration are shown in the ppt in attachment.
Thanks
Alain
At 14:58 07/01/2008, you wrote:
Is there a way to calculate or read feff7 or FEFF8 paths with the last version of Artemis? I could not find this information on this
On Sunday 06 January 2008 11:26:53 you wrote: page:
http://cars9.uchicago.edu/~ravel/software/aboutartemis.html
and this option is not listed in your to-do list. I suppose that there is a good reason for it!
Implementing the possibility to read at once several FEFF paths (for example from the list.dat file) could be useful, I think.
Alain,
I am CCing this general interest question to the mailing list.
Artemis does not actually have a preference for the version of feff that you use. Since Feff is run as an external process, all you need to do is configure Artemis to use your prefered version.
* In the Edit menu, select "Edit preferences".
* In the Atoms groups, change `template' to "feff7" or "feff8", as you wish. That will have the effect of changing what kind of feff.inp file atoms makes.
* In the Feff group, change `feff_executable' to the version of feff you are using. If the executable is not in the execution path, you will need to enter the fully resolved path as the value for that configuration parameter.
If you have run feff independently of Artemis and simply wish to import the feffNNNN.dat files, that should work with no regard to the version of Feff that you used. The format of the feffNNNN.dat file did not change between feff6 and feff8.
If you are seeing some particular failure of Artemis, then you will need to show me what happens. Without providing enough information for me to reproduce the problem on my own computer, it is not reasonable to expect that I can solve a problem.
HTH, B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973
My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Richard Mayes Barnes Group 450/452 Buehler Hall Department of Chemistry University of Tennessee Knoxville, TN 37996
Dear Alain, Although someone may have a better solution, you can run FEFF7 independently of Artemis then import the calculation results using the theory menu. This is what I do when using FEFF7, and I have never had a problem. Sincerely, Wayne Lukens Alain Manceau wrote:
Bruce,
Thank you for the clarification. I progressed, but still encounter a problem running FEFF7. The error message and the input parameters and configuration are shown in the ppt in attachment.
Thanks
Alain
At 14:58 07/01/2008, you wrote:
Is there a way to calculate or read feff7 or FEFF8 paths with the last version of Artemis? I could not find this information on this
On Sunday 06 January 2008 11:26:53 you wrote: page:
http://cars9.uchicago.edu/~ravel/software/aboutartemis.html
and this option is not listed in your to-do list. I suppose that there is a good reason for it!
Implementing the possibility to read at once several FEFF paths (for example from the list.dat file) could be useful, I think.
Alain,
I am CCing this general interest question to the mailing list.
Artemis does not actually have a preference for the version of feff that you use. Since Feff is run as an external process, all you need to do is configure Artemis to use your prefered version.
* In the Edit menu, select "Edit preferences".
* In the Atoms groups, change `template' to "feff7" or "feff8", as you wish. That will have the effect of changing what kind of feff.inp file atoms makes.
* In the Feff group, change `feff_executable' to the version of feff you are using. If the executable is not in the execution path, you will need to enter the fully resolved path as the value for that configuration parameter.
If you have run feff independently of Artemis and simply wish to import the feffNNNN.dat files, that should work with no regard to the version of Feff that you used. The format of the feffNNNN.dat file did not change between feff6 and feff8.
If you are seeing some particular failure of Artemis, then you will need to show me what happens. Without providing enough information for me to reproduce the problem on my own computer, it is not reasonable to expect that I can solve a problem.
HTH, B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973
My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
------------------------------------------------------------------------
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Hello everybody, Alain, as far as plot limits are concerned (the minor question in the .ppt): these are defined in the right panel of the main Artemis window, just above the box "document:plotting". If you want to vizualize the fit limit, you have to check the box near "window", also on this right panel, and then refresh plotting. A word on the apparent k-range for the fit, then; this range is defined from k-range(min)-dk/2 to k-Range(max)-dk/2, with k-range(min), k-range(max) and dk being defined in the "Fourier and fit parameters" subpanel. This range is defined so that the value of the apodization window equals 0.5 at k-range(min) and k-range(max) if you're using a Hamming window (or one of these classic ones). Best regards, Michel
Bruce,
Thank you for the clarification. I progressed, but still encounter a problem running FEFF7. The error message and the input parameters and configuration are shown in the ppt in attachment.
Thanks
Alain
At 14:58 07/01/2008, you wrote:
Is there a way to calculate or read feff7 or FEFF8 paths with the last version of Artemis? I could not find this information on this
On Sunday 06 January 2008 11:26:53 you wrote: page:
http://cars9.uchicago.edu/~ravel/software/aboutartemis.html
and this option is not listed in your to-do list. I suppose that there is a good reason for it!
Implementing the possibility to read at once several FEFF paths (for example from the list.dat file) could be useful, I think.
Alain,
I am CCing this general interest question to the mailing list.
Artemis does not actually have a preference for the version of feff that you use. Since Feff is run as an external process, all you need to do is configure Artemis to use your prefered version.
* In the Edit menu, select "Edit preferences".
* In the Atoms groups, change `template' to "feff7" or "feff8", as you wish. That will have the effect of changing what kind of feff.inp file atoms makes.
* In the Feff group, change `feff_executable' to the version of feff you are using. If the executable is not in the execution path, you will need to enter the fully resolved path as the value for that configuration parameter.
If you have run feff independently of Artemis and simply wish to import the feffNNNN.dat files, that should work with no regard to the version of Feff that you used. The format of the feffNNNN.dat file did not change between feff6 and feff8.
If you are seeing some particular failure of Artemis, then you will need to show me what happens. Without providing enough information for me to reproduce the problem on my own computer, it is not reasonable to expect that I can solve a problem.
HTH, B
-- Bruce Ravel ------------------------------------ bravel@bnl.gov
National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973
My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
------------------------------------------------------------------------
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On Tuesday 08 January 2008 12:34:00 Alain Manceau wrote:
Thank you for the clarification. I progressed, but still encounter a problem running FEFF7. The error message and the input parameters and configuration are shown in the ppt in attachment.
Hi Alain, I thought I would add a few thoughts to the very helpful feedback from Richard, Wayne, and Michel. I just tried artemis with feff7 and it works just fine on my computer. I did as I said -- I pointed artemis at the feff7 executable and changed the feff template to feff7. Feff7 ran and it wrote out feffNNNN.dat file which got imported properly. So it all seems fine to me -- although I should probably take a look-see on a windows machine to be sure everything works the same there. As a work-around, given the torubles you are seeing on your machine, I would suggest doing as Richard adn Wayne suggested and run feff7 outside of Artemis then import the results. As for the plotting question, I suspect there is not a problem, simply a disconnect with expectation. The numbers for k-range in the box labeled "Fourier and fit parameters" is the k-range used whenever a Fourier transform is made. It is also the fit range in k. The k-range shown in the lower right-hand corner of the Artemis window is the range over which the plot is made. All arrays in k are defined from 0 to the end of the input data range and the path arrays certainly contain data below there as Feff starts its calculationo at k=0. Thus the fit array contains data below the fit range even though the data outside that range does not contribute to the evaluation of the fitting metric. As Shelly Kelly often points out, if your fit resembles your data even outside the fitting range, that is an additional tidbit giving confidence in the appropriateness of your fitting model. HTH, B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Bruce,
I just tried artemis with feff7 and it works just fine on my computer. I did as I said -- I pointed artemis at the feff7 executable and changed the feff template to feff7. Feff7 ran and it wrote out feffNNNN.dat file which got imported properly. So it all seems fine to me -- although I should probably take a look-see on a windows machine to be sure everything works the same there.
I found the error. Feff7 was in the wrong directory: IFEFFFIT (together with a copy of feff6l) instead of BIN. Sorry for being thoughtless and the trouble.
As for the plotting question, I suspect there is not a problem, simply a disconnect with expectation. The numbers for k-range in the box labeled "Fourier and fit parameters" is the k-range used whenever a Fourier transform is made. It is also the fit range in k. The k-range shown in the lower right-hand corner of the Artemis window is the range over which the plot is made. All arrays in k are defined from 0 to the end of the input data range and the path arrays certainly contain data below there as Feff starts its calculationo at k=0. Thus the fit array contains data below the fit range even though the data outside that range does not contribute to the evaluation of the fitting metric. As Shelly Kelly often points out, if your fit resembles your data even outside the fitting range, that is an additional tidbit giving confidence in the appropriateness of your fitting model.
Yes, I understand this, but my question was much simple, actually. The plot in the ppt I sent yesterday (VG8) shows that the fit curve stops at 12.25 A-1 although kmax = 14.3 in the 'Fourier and Fit parameters' window. 12.25A-1 is the default upper limit for the forward FT and fit and when I change this value manually or in the preference (e.g., to 14.3), the plot still ends at 12.25 A-1. Alain
Did you check the data range and interpolation as I suggested?
mam
----- Original Message -----
From: "Alain Manceau"
Bruce,
I just tried artemis with feff7 and it works just fine on my computer. I did as I said -- I pointed artemis at the feff7 executable and changed the feff template to feff7. Feff7 ran and it wrote out feffNNNN.dat file which got imported properly. So it all seems fine to me -- although I should probably take a look-see on a windows machine to be sure everything works the same there.
I found the error. Feff7 was in the wrong directory: IFEFFFIT (together with a copy of feff6l) instead of BIN.
Sorry for being thoughtless and the trouble.
As for the plotting question, I suspect there is not a problem, simply a disconnect with expectation. The numbers for k-range in the box labeled "Fourier and fit parameters" is the k-range used whenever a Fourier transform is made. It is also the fit range in k. The k-range shown in the lower right-hand corner of the Artemis window is the range over which the plot is made. All arrays in k are defined from 0 to the end of the input data range and the path arrays certainly contain data below there as Feff starts its calculationo at k=0. Thus the fit array contains data below the fit range even though the data outside that range does not contribute to the evaluation of the fitting metric. As Shelly Kelly often points out, if your fit resembles your data even outside the fitting range, that is an additional tidbit giving confidence in the appropriateness of your fitting model.
Yes, I understand this, but my question was much simple, actually. The plot in the ppt I sent yesterday (VG8) shows that the fit curve stops at 12.25 A-1 although kmax = 14.3 in the 'Fourier and Fit parameters' window. 12.25A-1 is the default upper limit for the forward FT and fit and when I change this value manually or in the preference (e.g., to 14.3), the plot still ends at 12.25 A-1.
Alain
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Dear all, Using Atoms (latest version of Artemis), I tried to calculate a Feff input file based on a recently published structure for 6-Line Ferrihydrite (Michel et al, Science, 2007). Attached: Atoms input file generated with Artemis. For all three Fe sites as core (Fe1 and Fe2 octahedral, Fe3 tetrahedral), running Atoms yields Feff files with "overlapping atoms" located close to each other. The Artemis error messages after running Feff suggests that a shift vector may be needed in order to obtain correct Feff input files. As a "non-crystallographer", I would be grateful for advice on how this problem can be solved. Best regards, Andreas
Hi Andreas, The problem was that for the atoms in position 6c, the sum of x and y must be exactly 1. I have attached a corrected atoms.inp file that seems to work. Sincerely, Wayne Lukens Voegelin Andreas wrote:
Dear all,
Using Atoms (latest version of Artemis), I tried to calculate a Feff input file based on a recently published structure for 6-Line Ferrihydrite (Michel et al, Science, 2007).
Attached: Atoms input file generated with Artemis.
For all three Fe sites as core (Fe1 and Fe2 octahedral, Fe3 tetrahedral), running Atoms yields Feff files with "overlapping atoms" located close to each other. The Artemis error messages after running Feff suggests that a shift vector may be needed in order to obtain correct Feff input files.
As a "non-crystallographer", I would be grateful for advice on how this problem can be solved.
Best regards,
Andreas
------------------------------------------------------------------------
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! This atoms input file was generated by TkAtoms 3.0beta10 ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = 6L-Ferrihydrite title = Michel et al, Science, 2007 space = 186 a = 5.9280 b = 5.9280 c = 9.1260 alpha = 90.0 beta = 90.0 gamma = 120.0 core = Fe1 edge = K rmax = 4.0 shift 0.00000 0.00000 0.00000 atoms ! elem x y z tag occ. Fe 0.16950 0.83050 0.63650 Fe1 1.00000 Fe 0.33333 0.66667 0.33790 Fe2 1.00000 Fe 0.33333 0.66667 0.95950 Fe3 1.00000 O 0.00000 0.00000 0.04460 O1 1.00000 O 0.33333 0.66667 0.76340 O2 1.00000 O 0.16970 0.83030 0.24670 O3 1.00000 O 0.52270 0.47730 0.97960 O4 1.00000
On Thursday 10 January 2008 15:58:57 Wayne Lukens wrote:
The problem was that for the atoms in position 6c, the sum of x and y must be exactly 1. I have attached a corrected atoms.inp file that seems to work.
Wayne, That is exactly right. I am impressed. I didn't see that at all and I had my copy of the international tables open in front of me for the last half hour. The symmetry of that space group does indeed require what you say. And it provides Andreas with a work-around. I still think that Atoms should not have failed in that situation, however. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
Dear all,
Using Atoms (latest version of Artemis), I tried to calculate a Feff input file based on a recently published structure for 6-Line Ferrihydrite (Michel et al, Science, 2007).
Attached: Atoms input file generated with Artemis.
For all three Fe sites as core (Fe1 and Fe2 octahedral, Fe3 tetrahedral), running Atoms yields Feff files with "overlapping atoms" located close to each other. The Artemis error messages after running Feff suggests that a shift vector may be needed in order to obtain correct Feff input files.
As a "non-crystallographer", I would be grateful for advice on how
Hi Wayne and Bruce, It is amazing which difference 0.0001 Ang can make. Thank you both for your help! Best regards, Andreas -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Wayne Lukens Sent: Donnerstag, 10. Januar 2008 21:59 To: XAFS Analysis using Ifeffit Subject: Re: [Ifeffit] Atoms & Feff for Ferrihydrite Structure Hi Andreas, The problem was that for the atoms in position 6c, the sum of x and y must be exactly 1. I have attached a corrected atoms.inp file that seems to work. Sincerely, Wayne Lukens Voegelin Andreas wrote: this
problem can be solved.
Best regards,
Andreas
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Dear all Does anyone have cofe2o4 chi data by anychance or know where I can find the data? thanks a lot!! Best Regard. TaiYen Chen 979-739-7772 Department of Chemistry Texas A&M University P.O. Box 30012 College Station, TX 77842-3012 Visit us on the web at http://www.chem.tamu.edu
I have it. Anatoly -----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Tai-Yen Chen Sent: Monday, January 14, 2008 12:27 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] cofe2o4 chi data Dear all Does anyone have cofe2o4 chi data by anychance or know where I can find the data? thanks a lot!! Best Regard. TaiYen Chen 979-739-7772 Department of Chemistry Texas A&M University P.O. Box 30012 College Station, TX 77842-3012 Visit us on the web at http://www.chem.tamu.edu _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi, Anatoly
that is great,
can you mail me the file so that I can do some simulation.
thanks a lot!!
On Mon, 14 Jan 2008 12:32:56 -0500
"Frenkel, Anatoly"
I have it.
Anatoly
-----Original Message----- From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov]On Behalf Of Tai-Yen Chen Sent: Monday, January 14, 2008 12:27 PM To: XAFS Analysis using Ifeffit Subject: [Ifeffit] cofe2o4 chi data
Dear all Does anyone have cofe2o4 chi data by anychance or know where I can find the data? thanks a lot!!
Best Regard.
TaiYen Chen 979-739-7772 Department of Chemistry Texas A&M University P.O. Box 30012 College Station, TX 77842-3012
Visit us on the web at http://www.chem.tamu.edu _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
TaiYen Chen 979-739-7772 Department of Chemistry Texas A&M University P.O. Box 30012 College Station, TX 77842-3012 Visit us on the web at http://www.chem.tamu.edu
Dear all I have one question about crystal structure construction: our lab want to simulate exafs spectrum of CoFe2o4. For the normal spinel structure, the Co is at the Td site and Fe is at the Oh site. The number of ions (Co) in Td is only half amount of the ions (Fe) in Oh site. However, the case we are especially interested in is the inversed spinel form (which means we want to put the Co2+ in the Oh site). In this case, all the Td will be Fe, but the Oh will be Co+Fe. How can I create the atom page to do the theoretical calculation? Thanks!! TaiYen Chen 979-739-7772 Department of Chemistry Texas A&M University P.O. Box 30012 College Station, TX 77842-3012 Visit us on the web at http://www.chem.tamu.edu
You should start by reading S. Calvin et al, Phys. Rev. B 66, 224405 (2002) and question 14 at http://cars9.uchicago.edu/iffwiki/FAQ/FeffitModeling B On Tuesday 22 January 2008 18:21:50 Tai-Yen Chen wrote:
Dear all I have one question about crystal structure construction: our lab want to simulate exafs spectrum of CoFe2o4. For the normal spinel structure, the Co is at the Td site and Fe is at the Oh site. The number of ions (Co) in Td is only half amount of the ions (Fe) in Oh site. However, the case we are especially interested in is the inversed spinel form (which means we want to put the Co2+ in the Oh site). In this case, all the Td will be Fe, but the Oh will be Co+Fe. How can I create the atom page to do the theoretical calculation? Thanks!!
TaiYen Chen 979-739-7772 Department of Chemistry Texas A&M University P.O. Box 30012 College Station, TX 77842-3012
Visit us on the web at http://www.chem.tamu.edu _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
On Thursday 10 January 2008 15:00:19 Voegelin Andreas wrote:
Using Atoms (latest version of Artemis), I tried to calculate a Feff input file based on a recently published structure for 6-Line Ferrihydrite (Michel et al, Science, 2007).
Attached: Atoms input file generated with Artemis.
For all three Fe sites as core (Fe1 and Fe2 octahedral, Fe3 tetrahedral), running Atoms yields Feff files with "overlapping atoms" located close to each other. The Artemis error messages after running Feff suggests that a shift vector may be needed in order to obtain correct Feff input files.
As a "non-crystallographer", I would be grateful for advice on how this problem can be solved.
Andreas, I'm pretty sure I don't count as a crystallographer, and after looking into this problem, I'm not sure I am confortable calling myself a programmer either ;-) This atoms.inp file (which you copied verbatim from the Science article) triggers a bug I have never seen before in Atoms. When each unique crystal position is expanded to fill the unit cell, the symmetries of the cell will, in many cases, generate a particular position more than once. Atoms has an algorithm which catches those and throws away the repeats. It attempts to treat numerical precision correctly in the sense that two positions that differ by a very small fraction are considered the same. Typically that algorithm handles the level of numerical precision in cell constants and site coordinates given in the Science article without a problem (with the exception of the high symmetry 1/3 and 2/3 positions). In fact, I have never seen a situation where the algorithm failed as it did here -- and I have looked at a lot of atoms.inp files over the years. There is no work-around short of my fixing the algorithm in the next horae release. The only helpful thing I can think of is to attach three feff.inp files -- one for each Fe site -- to this message which I generated with a specially modified version of my demeter code base. That's not a very gratifying situation for either of us, but it should get you over the immediate hurdle. B -- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Methods Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 My homepage: http://xafs.org/BruceRavel EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
participants (9)
-
Alain Manceau -
Bruce Ravel -
Frenkel, Anatoly -
Matthew Marcus -
Michel Schlegel -
Richard Mayes -
Tai-Yen Chen -
Voegelin Andreas -
Wayne Lukens