[Ifeffit] Conflicting FEFF calculation

Robert Gordon ragordon at alumni.sfu.ca
Mon Apr 3 17:08:18 CDT 2017

Hi Ashis,

I can reproduce what you are seeing.
I exported the atoms.inp's for your two structures.

If I import TAA first and run atoms, it looks ok. I then import TPA and 
run - ok.
I re-run Atoms on TAA, it changes.

In fact, from a clean start of Artemis 0.9.25 on win10pro/AMD64, if I 
import TAA's inp and run it, it looks ok.
I added it again, it still looks ok, even if I re-run Atoms. I add TPA 
and run it, it looks ok, but if I rerun
either of the TAA, they have changed. Changes persist even if TPA discarded.

 From another clean start of Artemis, I import TAA and run Atoms - ok.
I import a different inp (ni metal) and run it - ok. Re-run TAA and it 
is ok.

 From another clean start, I import Ni metal and run it...ok
Import TPA and run it...ok...Rerun Ni and Ni changes...definite symmetry 
This symmetry change persists even if I discard TPA and import another 
copy of Ni.

Clean start, import Ni and run, then import another Rhombohedral 
structure (B phase)
and same problem...symmetry changes and I don't seem to be able to get 
it to change back,
even when I deliberately change the space group for Ni and it is the 
only calculation remaining.

Clean start...import Ni...ok....add rhombohedral structure (B) but don't 
run it..rerun Ni and Ni changes.

Clean start, import hexagonal structure (in P6)...ok...import 
Ni...ok....change hex to Rhomb indexed on hex
and Ni changes when rerun...

So...problem seems to be related to the symmetry - stuck in Rhombohedral 
once a R-structure
is added...or symmetry changed to R.

Haven't tried on Linux yet.


On 4/3/2017 1:46 PM, Ashis Biswas wrote:
> Dear Bruce,
> Sorry for late reply. I wanted to test in another computer before 
> replying. Unfortunately, this time also I got different results for 
> TAA. Following is the click by click description of what I am doing to 
> arrive in this state:
> Double click on “Atemis” shortcut on desktop => Click “add” in the 
> Feff calculation tab => Open “TPP” Atom input file from desktop=> 
> Click “Run Atom” => Click “Run Feff” => Click “add” in the Feff 
> calculation tab => Open “TAA” CIF file from desktop=> Click “Run Atom” 
> => Click “Run Feff”
> I am sorry for killing your time. Actually, I am very much new in this 
> field and therefore I really want to be sure that what I am doing for 
> importing object for feff calculation is correct or not. Thank you 
> very much for your support.
> With regards,
> Ashis
> On 2017-03-28 16:13, Bruce Ravel wrote:
>> On 03/27/2017 11:02 AM, Ashis Biswas wrote:
>>> Thank you very much for your reply. Here I am attaching two Artemis
>>> projects files (TAA_TPA and TPA_TAA), named according to their order of
>>> import. In my computer the paths for *TAA* are different in two project
>>> files. For example, i) in TAA_TPA project the Reff for three single
>>> scattering paths of O (@O1.1; @O3.1, and @O5.1) are different to 
>>> that in
>>> TPA_TAA project, ii) the single scattering path @C5.1 (path number 
>>> 6) at
>>> Reff of 2.682 A0 in TAA_TPA project is missing in TPA_TAA project, and
>>> so on.
>>> I am also attaching the papers from where the coordinates for TAA and
>>> TPA are obtained: TAA (Kamenar et al., 1993: tables 1 & 2; Fig. 1) and
>>> TPA (Pappalardo et al., 1983: Table 1; Fig. 1).
>> I agree that the TPA_TAA.fpj project file that you sent me has 
>> incorrect data in the Feff tab for TAA.
>> I have not, however, been able to reproduce that here.  And not for 
>> want of trying -- I spent the last half hour trying to find a way to 
>> replicate what you are showing in the TPA_TAA file. Regardless of the 
>> order in which I import the two structures and regardless of whether 
>> I have discarded and reimported Feff calculations, when I click the 
>> "Run Atoms" button on the TAA cif file, I /always/ get the structure 
>> from Table 4 in the Kamenar paper.  I cannot reproduce the Feff tab 
>> that you show in your TPA_TAA project file.
>> I have no idea how you got into the state you show in the TPA_TAA 
>> project.  It is clear that something went awry, but I don't know if 
>> it is an error of the program or of the user.  I can't fix a problem 
>> I can't observe.
>> I understand that this is not the answer you were looking for. I am 
>> simply not seeing the problem you are reporting.
>> B
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