Re: [Ifeffit] Primitive unit cell from .cif file
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.
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@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@millenia.cars.aps.anl.gov on behalf of joshua jason kas Sent: Thu 6/18/2009 2:41 PM To: ifeffit@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@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@millenia.cars.aps.anl.gov on behalf of joshua jason kas Sent: Wed 6/17/2009 2:16 PM To: ifeffit@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
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@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@millenia.cars.aps.anl.gov on behalf of joshua jason kas Sent: Thu 6/18/2009 2:41 PM To: ifeffit@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@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@millenia.cars.aps.anl.gov on behalf of joshua jason kas Sent: Wed 6/17/2009 2:16 PM To: ifeffit@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@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (2)
-
Carlo Segre -
joshua jason kas