There are two different input files which take the extension .inp. One is the feff.inp file, which is the input to FEFF and contains a list of coordinates (Cartesian, not crystallographic) of all atoms surrounding an absorpber atom out to a certain distance. ATOMS produces this. The other is an input file for ATOMS, which has a subset of the information found in a CIF file. ATOMS can save this out as well once you fill in the form, and you can thus re-use it if, for instance, you want to re-run ATOMS to produce a feff.inp file for a different site as absorber. ATOMS is the only program I know that produces FEFF files. mam On 8/9/2016 9:26 AM, Ed Han wrote:

I see. Thank you for the insight!

Is it possible to create the same .inp or .cif file in FEFF6 (or any of the FEFF versions) as well?

Or is the ATOMS program the most recommended software to perform this task?

Regards, Ed Han

On Mon, Aug 8, 2016 at 5:12 PM, Carlo Segre mailto:segre@iit.edu> wrote:

Hi Ed:

You do not need to start with a CIF file at all. All you need is the space group, the lattice constants and the atomic positions. You can then fillin the blanks for the Atoms program yourself.

Carlo

On Mon, 8 Aug 2016, Ed Han wrote:

Hello All,

I apologize in advance if this is not the correct method to reply to the thread.

Thank you for your replies and suggestions. I will look further into determining the atomic structure of the Hf-Al intermetallics through their papers.

Once I obtain this information, how do I go about creating the actual CIF file? Can I just open up any arbitrary CIF file and then change the parameters and name to match that of the Hf-Al systems?

Lastly, going through some CIF files from crystallography.net http://crystallography.net, I notice that some of the 3D models from the CIF has a different stoichiometry from the designated crystal. For example, I have attached a CIF file of SiO2 that I have found; however, the 3D representation only has 1 Silicon atom and 1 Oxygen atom. Do you have any insight on this disparity?

Regards, Ed Han

-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 tel:312.567.3498 Fax: 312.567.3494 tel:312.567.3494 segre@iit.edu mailto:segre@iit.edu http://phys.iit.edu/~segre segre@debian.org mailto:segre@debian.org

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This actually results in a bit of inconvenience - if you want to use ATOMS, you have to load some data into Artemis and pretend you want to analyze it. Another thing for a newbie to beware of - if you have inequivalent sites for your absorbing atom, you have to run ATOMS and FEFF separately for each of these, then add the resulting spectra in proportion determined by stoichiometry. If you use a program like Diamond, it tells you the Wyckoff notation (e.g. 12a meaning that a unit cell has 12 such atoms in it, even though they're specified once). I think ATOMS can produce a file with each atom listed explicitly (XYZ, I think) and you could count that. mam On 8/9/2016 10:35 AM, Scott Calvin wrote:

Hi Ed,

In case it’s not clear, ATOMS is built in to Artemis. (Long, long ago ATOMS was a separate program, so many people still refer to that functionality of Artemis by that name.)

—Scott Calvin Sarah Lawrence College

...

On Aug 9, 2016, at 12:40 PM, Matthew Marcus wrote:

There are two different input files which take the extension .inp. One is the feff.inp file, which is the input to FEFF and contains a list of coordinates (Cartesian, not crystallographic) of all atoms surrounding an absorpber atom out to a certain distance. ATOMS produces this. The other is an input file for ATOMS, which has a subset of the information found in a CIF file. ATOMS can save this out as well once you fill in the form, and you can thus re-use it if, for instance, you want to re-run ATOMS to produce a feff.inp file for a different site as absorber. ATOMS is the only program I know that produces FEFF files. mam

On 8/9/2016 9:26 AM, Ed Han wrote:

...

I see. Thank you for the insight!

Is it possible to create the same .inp or .cif file in FEFF6 (or any of the FEFF versions) as well?

Or is the ATOMS program the most recommended software to perform this task?

Regards, Ed Han

On Mon, Aug 8, 2016 at 5:12 PM, Carlo Segre mailto:segre@iit.edu> wrote:

Hi Ed:

You do not need to start with a CIF file at all. All you need is the space group, the lattice constants and the atomic positions. You can then fillin the blanks for the Atoms program yourself.

Carlo

On Mon, 8 Aug 2016, Ed Han wrote:

Hello All,

I apologize in advance if this is not the correct method to reply to the thread.

Thank you for your replies and suggestions. I will look further into determining the atomic structure of the Hf-Al intermetallics through their papers.

Once I obtain this information, how do I go about creating the actual CIF file? Can I just open up any arbitrary CIF file and then change the parameters and name to match that of the Hf-Al systems?

Lastly, going through some CIF files from crystallography.net http://crystallography.net, I notice that some of the 3D models from the CIF has a different stoichiometry from the designated crystal. For example, I have attached a CIF file of SiO2 that I have found; however, the 3D representation only has 1 Silicon atom and 1 Oxygen atom. Do you have any insight on this disparity?

Regards, Ed Han

-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 tel:312.567.3498 Fax: 312.567.3494 tel:312.567.3494 segre@iit.edu mailto:segre@iit.edu http://phys.iit.edu/~segre segre@debian.org mailto:segre@debian.org

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On Tue, Aug 9, 2016 at 1:07 PM, Bruce Ravel wrote:

On 08/09/2016 01:50 PM, Matthew Marcus wrote:

...

This actually results in a bit of inconvenience - if you want to use ATOMS, you have to load some data into Artemis and pretend you want to analyze it.

There is a "Stand-alone Atoms" item in the frickin' Start Menu. How does that constitute an inconvenience? If that's too many clicks for you, drag and drop a shortcut to the desktop.

You can use atoms from the command line to read an input or CIF file and write to a file or to standard output. You can use atoms from the command line with the "--wx" switch to fire up the stand-alone GUI app.

I acknowledge that the web app that died last January was widely used and that I am an unredeemable lay-about for not recreating it. But your criticism is a bit unfair, Matthew.

Oh, the WebAtoms problem is all me! --Matt

It is even pretty easy in the old Artemis. No need to load data just start from Theory and make a new Atoms input file then use the Theory menu to Write Special Output. Carlo On Tue, 9 Aug 2016, Matthew Marcus wrote:

Oh, the Demeter menu. I was looking in Artemis itself. Thanks! mam

On 8/9/2016 11:07 AM, Bruce Ravel wrote:

...

On 08/09/2016 01:50 PM, Matthew Marcus wrote:

...

This actually results in a bit of inconvenience - if you want to use ATOMS, you have to load some data into Artemis and pretend you want to analyze it.

There is a "Stand-alone Atoms" item in the frickin' Start Menu. How does that constitute an inconvenience? If that's too many clicks for you, drag and drop a shortcut to the desktop.

You can use atoms from the command line to read an input or CIF file and write to a file or to standard output. You can use atoms from the command line with the "--wx" switch to fire up the stand-alone GUI app.

I acknowledge that the web app that died last January was widely used and that I am an unredeemable lay-about for not recreating it. But your criticism is a bit unfair, Matthew.

B

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-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Interim Chair, Department of Chemistry Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org