[Ifeffit] Conflicting FEFF calculation

Tue Apr 4 09:07:46 CDT 2017

Robert, thanks for doing so much work to verify what Ashis is seeing.

That said, I am still not seeing this problem.  My working notion is 
that it is a problem that somehow got fixed while I was doing some other 
work a few months ago.

This morning, I prepared and uploaded a new installer package as a 
pre-release of the upcoming version.  Here's the direct link.

https://s3.amazonaws.com/demeter4xas/Demeter_0.9.26_with_Strawberry_Perl_(64)_pre2.exe

If one or both of you could install this and let me know if the problem 
persists, I would be grateful.

I did uncover a bunch of of problems with Demeter's crystallography bits 
while I was working on

    https://github.com/bruceravel/WebAtoms,
    http://millenia.cars.aps.anl.gov/webatoms

I don't really see the value of sifting through all that work to figure 
out what had an impact on Ashis' issue.  If the newer code works -- that 
seems good enough to me.

B

On 04/03/2017 06:08 PM, Robert Gordon wrote:
> 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
> change.
> 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.
>
> -R.
>
>
>
>
>
> 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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>
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-- 
  Bruce Ravel  ------------------------------------ bravel at bnl.gov

  National Institute of Standards and Technology
  Synchrotron Science Group at NSLS-II
  Building 743, Room 114
  Upton NY, 11973

  Homepage:    http://bruceravel.github.io/home/
  Software:    https://github.com/bruceravel
  Demeter:     http://bruceravel.github.io/demeter/