[Ifeffit] Bug when adding feff calculations

[Georges Siddiqi]

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
<patridge at buffalo.edu>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 at dyc.edu*
>
>
>
> On Oct 30, 2013, at 11:05 AM, Georges Siddiqi <gsiddiqi at gmail.com> 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 at gmail.com;
> Recipient: ifeffit at 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 <gsiddiqi at gmail.com>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
>>
>>
> <dartemis.log><Cu.inp><schrock 1.cif>
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