# [Ifeffit] Primitive unit cell from .cif file

Carlo Segre segre at iit.edu
Fri Jun 19 00:35:10 CDT 2009

```hi josh

On Thu, 18 Jun 2009, joshua jason kas wrote:

> Hi Bruce,
>> I don't really understand what you are driving at, but it seems as
>> though you want to express Diamond as a simple cubic cell with a two
>> atom basis?
>
> Yes, that would be the case for diamond, but for an arbitrary crystal
> structure specified as in a .cif I would like to find the primitive cell,
> i.e. the unit cell of smallest volume.
>

Actually, not cubic.  The primitive cell for diamond, which is FCC, is
rhombohedral and smaller than the cubic one.  The primitive vectors for
this cell in Carteisan coordinates are:

(0.5, 0.5, 0.0) x 3.5670 = (1.7835, 1.7835, 0.0000)
(0.5, 0.0, 0.5) x 3.5670 = (1.7835, 0.0000, 1.7835)
(0.0, 0.5, 0.5) x 3.5670 = (0.0000, 1.7835, 1.7835)

For the Diamond structure, there should be two atoms which fit in this
unit cell, one at (0, 0, 0) and another at (0.89175, 0.89175, 0.89175).

I hope that this is the information you need.

Carlo

>> I don't really understand how that
>> will save you time in
>> abinit, but, of course, I am not a crystallographer....
> Smaller volume means less bands to obtain the same energy range.
>
>> PS. Doesn't abinit understand crystal symmetry?
> Maybe. I couldn't get it to reproduce the diamond structure using only one
> atom in the cell, but I haven't been using it for very long, and will
> probably go to the abinit list for this.
>
>> Why can't you just tell it that it's diamond and has the symmetry of
>> diamond?
> For our application, we can't really use the symmetry at this point. Would
> be good if we can in the future, but for now we really need input that
> includes all atoms in the primitive unit cell.
>
> Again, thanks to everyone for your time. I hope this was not too far out
> in left field for this mailing list. Apologies if it was.
> Josh Kas
>
>>
>> --
>> Bruce Ravel  ----------------------------------- bravel at bnl.gov
>>
>> National Institute of Standards and Technology
>> Synchrotron Methods Group at Brookhaven National Laboratory
>> Building 535A
>> Upton NY, 11973
>>
>> My homepage:    http://cars9.uchicago.edu/~ravel
>> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>>
>>
>>
>>
>> -----Original Message-----
>> From: ifeffit-bounces at millenia.cars.aps.anl.gov on behalf of joshua jason kas
>> Sent: Thu 6/18/2009 2:41 PM
>> To: ifeffit at millenia.cars.aps.anl.gov
>> Subject: Re: [Ifeffit] Primitive unit cell from .cif file
>>
>> Thanks everyone for your suggestions! I have tried the following things.
>> I used atoms (webATOMS) to generate a p1.inp file using diamond as an
>> example, but this gives me the conventional cell with 8 atoms in
>> it instead of the 2 atom primitive cell. Am I doing something wrong?
>> The input file came from the atoms database and the output is as follows:
>>
>>  *
>>  *   "F d -3 m" appears in the International Tables with
>>  *   multiple choices of origin.  If the atoms list seems wrong, you
>>  *   should use a shift vector of:
>>  * 	-0.125, -0.125, -0.125
>>  *
>>  *
>> ! This p1.inp file was generated by WebAtoms 1.8 (Atoms 3.0beta10)
>> ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001
>> title =	name:     diamond
>> title =	formula:  C
>> title =	sites:    C1
>> title =	refer1:   Kittel, ISSP
>> title =	refer2:
>> title =	schoen:
>> title =	notes1:   diamond structure
>> space	p 1             ! original space group: F d -3 m
>> a =	  3.5670	b =	  3.5670	c =	  3.5670
>> alpha =	 90.0	beta =	 90.0	gamma =	 90.0
>> core =	C1_1	edge =	K	rmax =	  6.0
>> atoms
>> ! elem   x          y          z       tag             occ
>>   C     0.12500    0.12500    0.12500  C1_1           1
>>   C     0.12500    0.62500    0.62500  C1_2           1
>>   C     0.62500    0.12500    0.62500  C1_3           1
>>   C     0.62500    0.62500    0.12500  C1_4           1
>>   C     0.87500    0.37500    0.37500  C1_5           1
>>   C     0.87500    0.87500    0.87500  C1_6           1
>>   C     0.37500    0.37500    0.87500  C1_7           1
>>   C     0.37500    0.87500    0.37500  C1_8           1
>>
>> I also tried the Mercury demo, but all editing features are disabled.
>>
>> I will try Diamond now.
>>
>> Just to give some motivation here, I am working with abinit (along with
>> feff) to produce optical spectra. If I use a conventional cell, the
>> calculations become much more time consuming, so ideally I want to use a
>> primitive cell.
>> Thanks again for all your help!
>> Josh
>>
>>> Hi Josh,
>>>  You may try Diamond Demo version which is free.
>>>
>> I will give this a try.
>>
>>
>>>
>>> Hi Josh,
>>>
>>> If I understand your question, I think that Atoms does what you want.  Running the command line tool as "atoms -p" turns the attached cif file into the attached "p1.inp" file.  You can do the same thing inside of Artemis using "write special output" in the Theory menu.
>>
>>>
>>> B
>>>
>>> --
>>> Bruce Ravel  ----------------------------------- bravel at bnl.gov
>>>
>>> National Institute of Standards and Technology
>>> Synchrotron Methods Group at Brookhaven National Laboratory
>>> Building 535A
>>> Upton NY, 11973
>>>
>>> My homepage:    http://cars9.uchicago.edu/~ravel
>>> EXAFS software: http://cars9.uchicago.edu/~ravel/software/exafs/
>>>
>>>
>>>
>>>
>>> -----Original Message-----
>>> From: ifeffit-bounces at millenia.cars.aps.anl.gov on behalf of joshua jason kas
>>> Sent: Wed 6/17/2009 2:16 PM
>>> To: ifeffit at millenia.cars.aps.anl.gov
>>> Subject: [Ifeffit] Primitive unit cell from .cif file
>>>
>>> Hi everyone,
>>> I was wondering if there is a simple (free) utility for producing a
>>> primitive cell (not conventional) from an asymmetric cell and space group.
>>> Basically, I want to be able to easily go from a crystallographic
>>> information file to a primitive unit cell. I know that there are ways to
>>> do this within applications like material studio, but these are expensive.
>>> Any help would be appreciated.
>>> Thanks,
>>> Josh Kas
>>> _______________________________________________
>>> Ifeffit mailing list
>>> Ifeffit at millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>>
>>>
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>>> ------------------------------
>>>
>>> Message: 4
>>> Date: Wed, 17 Jun 2009 23:40:10 -0300
>>> From: Eugenio Otal <eugenioh at gmail.com>
>>> To: ifeffit at millenia.cars.aps.anl.gov
>>> Message-ID:
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> Hi,
>>> I performed EXAFS simulation and want to obtain the radial distribution of
>>> the signal. I tried with athena but I cannot process it like experimental
>>> signal.
>>> Is there any trick to transform the signal into radial distribution?
>>> Thanks, euG
>>>
>>> 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -
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>>> ------------------------------
>>>
>>> Message: 5
>>> Date: Wed, 17 Jun 2009 23:57:18 -0300
>>> From: Eugenio Otal <eugenioh at gmail.com>
>>> Subject: [Ifeffit] Primitive unit cell from .cif file
>>> To: ifeffit at millenia.cars.aps.anl.gov
>>> Message-ID:
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> Josh,
>>> you can also try with Mercury, has a free version at:
>>> http://www.ccdc.cam.ac.uk/products/mercury/
>>> Hope it helps, euG
>>>
>>>
>>>
>>>
>>>
>>> 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -
>>>
>>> Hi Josh,
>>>  You may try Diamond Demo version which is free.
>>>
>>>
>>> Good luck,
>>>
>>> Mengqiang Zhu
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> -----------------------
>>> Mengqiang Zhu
>>> Ph.D Candidate
>>> Environmental Soil Chemistry
>>> Department of Plant and Soil Sciences
>>> University of Delaware
>>> 152 Townsend Hall
>>> Newark, DE 19716
>>> http://ag.udel.edu/soilchem/zhu.html
>>>
>>>
>>> ---- Original message ----
>>>> *Date: Wed, 17 Jun 2009 11:16:49 -0700 (PDT)
>>> *>*From: ifeffit-bounces at millenia.cars.aps.anl.gov
>>> <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit> (on behalf
>>> of joshua jason kas <hebhop at u.washington.edu
>>> <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>>)
>>> *>*Subject: [Ifeffit] Primitive unit cell from .cif file
>>> *>*To: ifeffit at millenia.cars.aps.anl.gov
>>> <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
>>> *>*
>>> *>*Hi everyone,
>>> *>*I was wondering if there is a simple (free) utility for producing a
>>> *>*primitive cell (not conventional) from an asymmetric cell and space group.
>>> *>*Basically, I want to be able to easily go from a crystallographic
>>> *>*information file to a primitive unit cell. I know that there are ways to
>>> *>*do this within applications like material studio, but these are expensive.
>>> *>*Any help would be appreciated.
>>> *>*Thanks,
>>> *>*Josh Kas
>>> *>*_______________________________________________
>>> *>*Ifeffit mailing list
>>> *>*Ifeffit at millenia.cars.aps.anl.gov
>>> <http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit>
>>> *>*http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>> *
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>>> ------------------------------
>>>
>>> Message: 6
>>> Date: Thu, 18 Jun 2009 07:51:38 -0700
>>> From: "Kelly, Shelly" <Shelly.Kelly at uop.com>
>>> Subject: Re: [Ifeffit] Radial distribution
>>> To: "XAFS Analysis using Ifeffit" <ifeffit at millenia.cars.aps.anl.gov>
>>> Message-ID:
>>> 	<5A8CCCCD35FC0946BE602D2F43C0218A0EA7A3 at AZ18EV808.global.ds.honeywell.com>
>>>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>>
>>> Hi Eug,
>>>
>>> I'm not sure that I understand your question. Do you mean that your ran FEFF and want to plot the magnitude of the Fourier transform of the FEFF calculation?  If so, you will want to use Artemis for that.   There is information about how to use Artemis on the tutorials page of www.xafs.org. Please ask again, if I misunderstood.
>>>
>>> Cheers,
>>> Shelly
>>>
>>> -----Original Message-----
>>> From: ifeffit-bounces at millenia.cars.aps.anl.gov on behalf of Eugenio Otal
>>> Sent: Wed 6/17/2009 9:40 PM
>>> To: ifeffit at millenia.cars.aps.anl.gov
>>>
>>> Hi,
>>> I performed EXAFS simulation and want to obtain the radial distribution of
>>> the signal. I tried with athena but I cannot process it like experimental
>>> signal.
>>> Is there any trick to transform the signal into radial distribution?
>>> Thanks, euG
>>>
>>> 8<- - - - - - 8<- - - - - - 8<- - - - - - 8<- - - - - -
>>>
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>>>
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--
Carlo U. Segre -- Professor of Physics