[Ifeffit] Primitive unit cell from .cif file
Ravel, Bruce
bravel at bnl.gov
Thu Jun 18 14:37:53 CDT 2009
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? Isn't that Pm3m with atoms at 0,0,0 and 1/4,1/4,1/4, or some such. I don't really understand how that will save you time in abinit, but, of course, I am not a crystallographer....
B
PS. Doesn't abinit understand crystal symmetry? Why can't you just tell it that it's diamond and has the symmetry of diamond?
--
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.
>
> http://www.crystalimpact.com/diamond/download.htm
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>
> Subject: [Ifeffit] Radial distribution
> To: ifeffit at millenia.cars.aps.anl.gov
> Message-ID:
> <da22ad30906171940k5d3e3fe9td06c60aba4eccecc at mail.gmail.com>
> 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:
> <da22ad30906171957j270038bfh7a8088c6c5807258 at mail.gmail.com>
> 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.
>
> http://www.crystalimpact.com/diamond/download.htm
>
> 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
> Subject: [Ifeffit] Radial distribution
>
> 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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> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
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>
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