[Ifeffit] Problem Importing CIF files into Larch

[Matt Newville]

Hi Vincent,

Yeah - we are using pymatgen to do the actual CIF parsing, and I think that
part is working fine.  Well, except that it isn't great at identifying
equivalent positions and so tends to give at least 2x more sites than
actually necessary.  In itself, that isn't a huge problem.

The problem that Amol (and, I'm guessing you saw too) was that structures
generated by pymatgen or CrystalMaker, etc won't have some of the fields
currently expected. I started with a restricted set from the AmMin
Database, and was focused on searching through these, so just assumed that
each structure would have a publication -- that is also true for structures
from COD, but won't be true for structures from CrystalMaker or ShelXL.
And right now, the CIF Browser wants to take any CIF you read in and add it
to the database (so you'll have it next time).   But, it should not assume
the CIF file will have all that information....

That's all to say that I think this is fixable....




On Mon, Aug 16, 2021 at 3:31 PM Vincent Wu <vincentwu at ucsb.edu> wrote:

> Hello,
>
> I've found that if I have cif files that don't work with Larch, I use
> Pymatgen to read the CIF and output a Pymatgen generated CIF, which would
> then work with Larch. I believe that Pymatgen cleans up cifs in a way, so
> that they become compatible.
>
> Vincent
>
> On Mon, Aug 16, 2021 at 1:22 PM Matt Newville <newville at cars.uchicago.edu>
> wrote:
>
>> Hi Amol,
>>
>> Sorry for the delay, I was offline most of last week.   Thanks for
>> posting these CIF files.
>> I think these should be usable -- the basic "cif2feffinp()" function
>> works on these to generate a valid Feff.inp,  but the GUI CIF Browser is
>> currently expecting additional fields such as publication information.  I
>> guess those fields should be optional.   I think there is another issue
>> with using multi-site CIF structures that I want to look into.
>> So, I hope to get this fixed soon, but I also want to tackle a few other
>> issues before posting a completely new version.
>>
>> --Matt
>>
>>
>> On Tue, Aug 10, 2021 at 4:12 PM <amolagarwal2025 at u.northwestern.edu>
>> wrote:
>>
>>> Hi,
>>>
>>> I hope you are doing well. I am writing regarding some issues that I am
>>> having with opening my CIF files in Larch. I have used these same CIF files
>>> in the past in Artemis to run feff calculations. When I open these files in
>>> the Larch open feff tab, it shows a dialog box saying that there is an
>>> error opening the CIF file. This is happening with all my CIF files and I
>>> am not sure why. I am attaching a couple of these CIF files. I would really
>>> appreciate some help on this.
>>>
>>>
>>>
>>> Amol Agarwal
>>>
>>> PhD Student
>>>
>>> Materials Science & Engineering | Northwestern University
>>>
>>>
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-- 
--Matt Newville <newville at cars.uchicago.edu> 630-327-7411
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