dear listhost, I would like to use Artemis/Atoms to simulate EXAFS of a crystalline material with significant defects that include additional atoms to the unit cell. Can I simulate this material without making a new cif file? Ideally, I would be able to input a DFT-optimized model cluster as xyz coordinates only -- no crystallographic information. This problem seems analogous to modeling discrete molecules. Can molecules be simulated by atoms/artemis? I know FEFF is capable of this, but I would like to use atoms for making my input file for feff. Carl -- PhD Candidate | Chemistry | MIT SB | 2010 | University of Chicago
Hi Carl, You can always use symmetry P1 and specify every atom in the unit cell in the atoms input. That can be tedious for a large unit cell, but is achievable. -R. On 10/31/2013 11:09 AM, Carl Brozek wrote:
dear listhost,
I would like to use Artemis/Atoms to simulate EXAFS of a crystalline material with significant defects that include additional atoms to the unit cell.
Can I simulate this material without making a new cif file? Ideally, I would be able to input a DFT-optimized model cluster as xyz coordinates only -- no crystallographic information.
This problem seems analogous to modeling discrete molecules. Can molecules be simulated by atoms/artemis? I know FEFF is capable of this, but I would like to use atoms for making my input file for feff.
Carl
-- PhD Candidate | Chemistry | MIT SB | 2010 | University of Chicago
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E Argonne, IL, USA 60439 630-252-0581 630-252-0580 fax
YOu could use ATOMS to make a FEFF file for a simple structure, then copy the header from that and replace the atoms list with a set of coordinates. You'd have to write a program which would automatically fill in the correct IPOTs and symbols, but it's not that hard. What's annoying is if you have multiple inequivalent absorber atoms, because then you have to make individual FEFF files centered about each one and run FEFF multiple times. I know that the CFAVERAGE card is supposed to take care of that, but I gather that it doesn't work for XANES. Anyone have an idea how reliable it is for EXAFS? mam On 10/31/2013 9:19 AM, Robert Gordon wrote:
Hi Carl,
You can always use symmetry P1 and specify every atom in the unit cell in the atoms input.
That can be tedious for a large unit cell, but is achievable.
-R.
On 10/31/2013 11:09 AM, Carl Brozek wrote:
dear listhost,
I would like to use Artemis/Atoms to simulate EXAFS of a crystalline material with significant defects that include additional atoms to the unit cell.
Can I simulate this material without making a new cif file? Ideally, I would be able to input a DFT-optimized model cluster as xyz coordinates only -- no crystallographic information.
This problem seems analogous to modeling discrete molecules. Can molecules be simulated by atoms/artemis? I know FEFF is capable of this, but I would like to use atoms for making my input file for feff.
Carl
-- PhD Candidate | Chemistry | MIT SB | 2010 | University of Chicago
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Dr. Robert Gordon Staff Scientist, PNCSRF APS Sector 20 (PNC/XSD) 9700 S Cass Ave. 435E Argonne, IL, USA 60439
630-252-0581 630-252-0580 fax
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Hi Carl: Yes, you can do that and start with a FEFF input file if you know the coordinates of all the atoms that you need in your model. After you edit the FEFF input file, you can simply start from there bypassing the atoms portion of the model building. Carlo On Thu, 31 Oct 2013, Carl Brozek wrote:
dear listhost,
I would like to use Artemis/Atoms to simulate EXAFS of a crystalline material with significant defects that include additional atoms to the unit cell.
Can I simulate this material without making a new cif file? Ideally, I would be able to input a DFT-optimized model cluster as xyz coordinates only -- no crystallographic information.
This problem seems analogous to modeling discrete molecules. Can molecules be simulated by atoms/artemis? I know FEFF is capable of this, but I would like to use atoms for making my input file for feff.
Carl
-- Carlo U. Segre -- Duchossois Leadership Professor of Physics Director, Center for Synchrotron Radiation Research and Instrumentation Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@iit.edu http://phys.iit.edu/~segre segre@debian.org
Carl, See https://speakerdeck.com/bruceravel/modeling-non-crystalline-samples particularly the bit on slides 11 and 12. The bottom line is that Atoms is *a* starting point, not *the* starting point. It is just one way of making input data for Feff, not the only way. B On 10/31/2013 12:09 PM, Carl Brozek wrote:
dear listhost,
I would like to use Artemis/Atoms to simulate EXAFS of a crystalline material with significant defects that include additional atoms to the unit cell.
Can I simulate this material without making a new cif file? Ideally, I would be able to input a DFT-optimized model cluster as xyz coordinates only -- no crystallographic information.
This problem seems analogous to modeling discrete molecules. Can molecules be simulated by atoms/artemis? I know FEFF is capable of this, but I would like to use atoms for making my input file for feff.
Carl
-- PhD Candidate | Chemistry | MIT SB | 2010 | University of Chicago
_______________________________________________ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
-- Bruce Ravel ------------------------------------ bravel@bnl.gov National Institute of Standards and Technology Synchrotron Science Group at NSLS --- Beamlines U7A, X24A, X23A2 Building 535A Upton NY, 11973 Homepage: http://xafs.org/BruceRavel Software: https://github.com/bruceravel
participants (5)
-
Bruce Ravel -
Carl Brozek -
Carlo Segre -
Matthew Marcus -
Robert Gordon