[Ifeffit] Ifeffit Digest, Vol 222, Issue 2

Tue Aug 17 06:45:05 CDT 2021

Hi everybody, 

I would like to draw your attention to the following postdoc position: 

https://www.pse.kit.edu/karriere/joboffer.php?id=85889&language=en

It will be great if you forward it to suitable candidates. 

Thank you in advance and best from me, 

Tonya

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Gesendet: Montag, 16. August 2021 23:46
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Betreff: Ifeffit Digest, Vol 222, Issue 2

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Today's Topics:

   1. Re: Problem Importing CIF files into Larch (Matt Newville)
   2. Re: Problem Importing CIF files into Larch (Vincent Wu)
   3. Re: Problem Importing CIF files into Larch (Matt Newville)

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Message: 1
Date: Mon, 16 Aug 2021 15:21:13 -0500
From: Matt Newville <newville at cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Problem Importing CIF files into Larch
Message-ID:
	<CA+7ESbrWMTGYTa+T+2u+++Qz92JQyTJFDqsFkhVZCCqMQfiXhw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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
>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
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Message: 2
Date: Mon, 16 Aug 2021 13:30:44 -0700
From: Vincent Wu <vincentwu at ucsb.edu>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Problem Importing CIF files into Larch
Message-ID:
	<CAHd9kXoSNt15f0P5c5P9wjTDKRfGjW6nqFOQngcdm7dFm=XNBg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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
>>
>>
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>>
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
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Message: 3
Date: Mon, 16 Aug 2021 16:45:20 -0500
From: Matt Newville <newville at cars.uchicago.edu>
To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
Subject: Re: [Ifeffit] Problem Importing CIF files into Larch
Message-ID:
	<CA+7ESbpjyP3+6gs_5GdR1mLS5vWHbk06Kpohutbaz3zDJPc1hQ at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"

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
>>>
>>>
>>> _______________________________________________
>>> Ifeffit mailing list
>>> Ifeffit at millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>> Unsubscribe: 
>>> http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>>>
>>
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>>
> _______________________________________________
> Ifeffit mailing list
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> Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit
>

--
--Matt Newville <newville at cars.uchicago.edu> 630-327-7411
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