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
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@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
Hello all, I'm applying the principle of interpolation in order to find the buckling angle in a similar system to the lead titanate example. And though I'm sure that my path.dat list contains paths of identical reff, my generated feffNNNN.dat files are changing the path lengths for beta=0 and beta=20. I think it has something to do with rounding in feff - am i right? See below - FEFF1019 = beta 0 degrees, FEFF2019 = beta 20 degrees, and relevant part of paths.dat file. Thanks for your assistance! Joseph ---------------> FROM FEFF2019.dat 4 4.000 5.9211 3.6223 -3.72616 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# 0.0000 0.0000 0.0000 0 32 Ge absorbing atom 0.0000 -2.9590 0.0000 1 52 Te 0.0000 -5.7395 -1.0213 2 51 Sb 0.0000 -2.9590 0.0000 1 52 Te ------------------> FROM FEFF1019.dat 4 4.000 5.9179 3.6223 -3.72616 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# 0.0000 0.0000 0.0000 0 32 Ge absorbing atom 0.0000 -2.9590 0.0000 1 52 Te 0.0000 -5.9179 0.0000 2 51 Sb 0.0000 -2.9590 0.0000 1 52 Te -------------------------------> FROM PATHS LIST 1019 4 4.000 index, nleg, degeneracy, r= 5.9179 x y z ipot label rleg beta eta 0.000000 -2.958950 0.000000 1 'Te ' 0.000000 -5.917900 0.000000 2 'Sb ' 0.000000 -2.958950 0.000000 1 'Te ' 0.000000 0.000000 0.000000 0 'Ge ' 2019 4 4.000 index, nleg, degeneracy, r= 5.9179 x y z ipot label rleg beta eta 0.000000 -2.958950 0.000000 1 'Te ' 0.000000 -5.739453 -1.021255 2 'Sb ' 0.000000 -2.958950 0.000000 1 'Te ' 0.000000 0.000000 0.000000 0 'Ge ' -- Joseph Washington Research Assistant Department of Physics North Carolina State University 431 Riddick Hall Raleigh, NC 27695-8202 email: jswashin@ncsu.edu
Hi Joseph,
I think this thread may have gone under-noticed, so sorry for not responding.
This seems like a really strange situation (how could Feff be getting
path distances wrong??), but I suspect from your message that you may
have been deliberately playing with the intermediate Feff files and
re-running certain modules. In that case, it would be possible to
get these seemingly inconsistent results. For example, is it
possible that you deliberately moved the Sb atom from
0.0000 -5.7395 -1.0213 2 51 Sb
to
0.0000 -5.9179 0.0000 2 51 Sb
after running through the full calculation once, and then only running
the path finder and genfmt on the distorted structure?
That is: can you explain what you did in more detail?
Thanks,
--Matt
On Fri, Jun 19, 2009 at 10:19 AM, Joseph Washington
Hello all, I'm applying the principle of interpolation in order to find the buckling angle in a similar system to the lead titanate example. And though I'm sure that my path.dat list contains paths of identical reff, my generated feffNNNN.dat files are changing the path lengths for beta=0 and beta=20. I think it has something to do with rounding in feff - am i right? See below - FEFF1019 = beta 0 degrees, FEFF2019 = beta 20 degrees, and relevant part of paths.dat file.
Thanks for your assistance!
Joseph
---------------> FROM FEFF2019.dat 4 4.000 5.9211 3.6223 -3.72616 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# 0.0000 0.0000 0.0000 0 32 Ge absorbing atom 0.0000 -2.9590 0.0000 1 52 Te 0.0000 -5.7395 -1.0213 2 51 Sb 0.0000 -2.9590 0.0000 1 52 Te
------------------> FROM FEFF1019.dat 4 4.000 5.9179 3.6223 -3.72616 nleg, deg, reff, rnrmav(bohr), edge x y z pot at# 0.0000 0.0000 0.0000 0 32 Ge absorbing atom 0.0000 -2.9590 0.0000 1 52 Te 0.0000 -5.9179 0.0000 2 51 Sb 0.0000 -2.9590 0.0000 1 52 Te
-------------------------------> FROM PATHS LIST 1019 4 4.000 index, nleg, degeneracy, r= 5.9179 x y z ipot label rleg beta eta 0.000000 -2.958950 0.000000 1 'Te ' 0.000000 -5.917900 0.000000 2 'Sb ' 0.000000 -2.958950 0.000000 1 'Te ' 0.000000 0.000000 0.000000 0 'Ge '
2019 4 4.000 index, nleg, degeneracy, r= 5.9179 x y z ipot label rleg beta eta 0.000000 -2.958950 0.000000 1 'Te ' 0.000000 -5.739453 -1.021255 2 'Sb ' 0.000000 -2.958950 0.000000 1 'Te ' 0.000000 0.000000 0.000000 0 'Ge '
-- Joseph Washington Research Assistant Department of Physics North Carolina State University 431 Riddick Hall Raleigh, NC 27695-8202 email: jswashin@ncsu.edu _______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
participants (4)
-
Joseph Washington -
joshua jason kas -
Matt Newville -
Ravel, Bruce