Re: [Ifeffit] Bug when adding feff calculations

thanks for noticing that! The program I'm using (Mercury), only shows the molecule, so I guess that's why I never thought of that. thanks again, georges On Wed, Oct 30, 2013 at 5:04 PM, Christopher Patridge wrote:

Hi Georges,

If I import the cif file into VESTA, it shows two W atoms in the unit cell explaining the addition of the second W potential in the list; attached below. The cif file only includes half of the atoms in the unit cell so it is not really a bug.

******************************************** Dr. Christopher Patridge Assistant Professor of Chemistry Dept of Math and Natural Science D'youville College 320 Porter Ave., Buffalo, NY 14201 Phone: 716-829-8096 Email: *patridgc@dyc.edu*

On Oct 30, 2013, at 11:05 AM, Georges Siddiqi wrote:

sorry to spam, but I just received an automated message saying that the attachments were blocked because of the athena file I included:

The Copper foil.fpj has been blocked, and Quarantine entire message has been taken on 10/30/2013 9:58:21 AM. Message details: Server: LUCKMAN Sender: gsiddiqi@gmail.com; Recipient: ifeffit@millenia.cars.aps.anl.gov; Subject: [Ifeffit] Bug when adding feff calculations Attachment name: Copper foil.fpj

in case the other attachments were blocked as well, I'm reattaching them.

is there a way to attach athena/artemis files without having the servers block them?

thanks, georges

On Wed, Oct 30, 2013 at 3:55 PM, Georges Siddiqi wrote:

...

Hi,

I'd like to report 2 bugs that I have when dealing with Feff calculations. One is critical (program crashes), the other is more troublesome, but i've found ways around it.

OS: Windows 7, SP1 Demeter version: 0.9.18

*1) Critical - Trying to add single scattering paths of arbitrary lengths. This used to work with an older version of the program, but now, no matter what I do, when I add a single scattering path with any length, the program crashes*

I've attached the log file (dartemis.log)* * * * How to replicate: -import any file (i've attached Cu.inp for ease of comparison) -run atoms -run feff -load an athena file (i've attached Cu foil.apj) -go to "Path like" tab -input any bond distance, and drag path over to the path list *-*program should crash

This problem occurs both with cif files and inp files (and several of both file types have been tried), and (so far) any type of data set I try to import into athena. I've just chosen the attached files for their simplicity.

2) Not critical - I deal with a lot of organometallic compounds whose cif files correspond of only 1 absorbing atom surrounded by a network of non-absorbing atoms. i.e. not a regular, repeating lattice.* *When I import the cif file for one of these compounds (*see attachment, schrock 1.cif*), the Atoms page is fine, but in the Feff page, the "potentials" lists the absorbing atom as ipot 0 and 1: POTENTIALS * ipot Z tag 0 74 W 1 74 W 2 8 O 3 7 N 4 6 C 5 1 H while in the atoms list, it only appears once as ipot 0. Naturally, if I just click "run Feff", the program returns an error.

My workaround to this has been to copy the atoms list into notepad, save, import into excel, subtract 1 from the ipot column (besides ipot 0), and replace the old atoms list with the corrected atoms list. then I manually change the potentials to: POTENTIALS * ipot Z tag 0 74 W 1 8 O 2 7 N 3 6 C 4 1 H

after this it works fine.

So this isn't a big burden, after a bit of practice I've gotten pretty fast at editing the Feff file, but if there's some easier solution it would be great.

This problem occurs with any monomeric compounds. If I run the feff on a dimeric organometallic compound, there's no problems.

Please let me know if there's any additional information I can supply that would help with this.

thanks, Georges Siddiqi

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