Inconsistency in generaton of feff.inp by atoms
Bruce: I have just run up against an odd error in atoms. I am not sure why it happens but it is consistent among all my computers. I start tkatoms and set up a structural model fo rthe wurtzite structure as follows: ----------------- atoms.inp ---------------- ! This atoms input file was generated by TkAtoms 3.0beta8 ! Atoms written by and copyright (c) Bruce Ravel, 1998-2001 title = ZnS Wurtzite structure space = p 63 m c a = 3.820 b = 3.820 c = 6.260 alpha = 90.0 beta = 90.0 gamma = 120.0 core = Zn edge = K rmax = 7.0 shift 0.0000 0.0000 0.0000 atoms ! elem x y z tag occ. Zn 0.3333 0.6667 0.0000 1.0000 S 0.3333 0.6667 0.3748 1.0000 ----------------- Then I run atoms from within tkatoms and get a feff.inp file: ----------------- first feff.inp (top lines only)---------------- * This feff input file was generated by TkAtoms 3.0beta8 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 761.06 cm^-1, delta_mu = 589.98 cm^-1 * specific gravity = 4.091 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction: 0.00045 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE ZnS Wurtzite structure HOLE 1 1.0 * Zn K edge (9659.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 7.0 *CRITERIA curved plane *DEBYE temp debye-temp *NLEG 8 POTENTIALS * ipot Z element 0 30 Zn 1 30 Zn 2 16 S ATOMS * this list contains 68 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Zn 0.00000 2.20546 0.00004 -0.78375 2 S_1 2.34058 -1.10276 -1.90996 -0.78375 2 S_1 2.34058 -1.10276 1.91004 -0.78375 2 S_2 2.34064 0.00000 0.00000 2.34625 2 S_3 2.34625 3.30822 1.91000 0.00000 1 Zn_1 3.82000 -3.30822 1.91000 0.00000 1 Zn_1 3.82000 0.00000 3.82000 0.00000 1 Zn_1 3.82000 3.30822 -1.91000 0.00000 1 Zn_1 3.82000 -3.30822 -1.91000 0.00000 1 Zn_1 3.82000 0.00000 -3.82000 0.00000 1 Zn_1 3.82000 ----------------------------- Then I save the atoms.inp file and when I read it in again and run atoms, I get a completely different result: ------------------- second feff.inp (top lines only) -------------- * This feff input file was generated by Atoms 3.0beta8 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * total mu = 1522.11 cm^-1, delta_mu = 1179.96 cm^-1 * specific gravity = 8.182 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * * Normalization correction: 0.00045 ang^2 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * TITLE ZnS Wurtzite structure HOLE 1 1.0 * Zn K edge (9659.0 eV), second number is S0^2 * mphase,mpath,mfeff,mchi CONTROL 1 1 1 1 PRINT 1 0 0 0 RMAX 7.0 *CRITERIA curved plane *DEBYE temp debye-temp *NLEG 8 POTENTIALS * ipot Z element 0 30 Zn 1 30 Zn 2 16 S ATOMS * this list contains 136 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Zn 0.00000 0.00011 0.00006 0.00000 1 Zn_1 0.00013 -1.10274 1.90987 -0.78375 2 S_1 2.34049 -1.10274 -1.90987 -0.78375 2 S_1 2.34049 2.20548 0.00013 -0.78375 2 S_2 2.34060 2.20548 -0.00013 -0.78375 2 S_2 2.34060 -1.10274 1.91013 -0.78375 2 S_3 2.34070 -1.10274 -1.91013 -0.78375 2 S_3 2.34070 0.00000 0.00000 2.34625 2 S_4 2.34625 0.00011 0.00006 2.34625 2 S_4 2.34625 -3.30811 -1.90994 0.00000 1 Zn_2 3.81987 -3.30811 1.91006 0.00000 1 Zn_3 3.81994 0.00011 -3.81994 0.00000 1 Zn_3 3.81994 3.30822 1.91000 0.00000 1 Zn_4 3.82000 ----------------------------------------------- You can see that the total mu, specific gravity and delta mu are different! I can run atoms from teh command line as well and I get the same incorrect result. I am running atoms-3.0beta8 but I tested beta9 and got the same result. I don't have this problem with the zincblende structure which is cubic so there must be a problem with the hexagonal lattice. Carlo -- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@agni.phys.iit.edu http://www.iit.edu/~segre
Hi Carlo,
could this be the same bug we discussed on the list in may (incorrect
setting of the angles when reading hexagonal structures, see below)?
Have you tried the "workaround" of manually reentering the correct
angles each time?
Best, Peter
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Date: Wed, 21 May 2003 14:22:33 -0500 (CDT)
From: "Carlo U. Segre"
Hello Peter: I tried your suggestion but the only way I could get the program to produce the correct atom positions, was to delete the old atoms and re-enter them. This is all that is required to fix the error. What concerns me more is that when I run the command line version of the program with the input file that I showed in my previous email, atoms gives the incorrect results. I can on ly conclude that there is something funny about the way the atom positions are read in in this case. Carlo On Tue, 4 Nov 2003, Peter Pfalzer wrote:
Hi Carlo,
could this be the same bug we discussed on the list in may (incorrect setting of the angles when reading hexagonal structures, see below)? Have you tried the "workaround" of manually reentering the correct angles each time?
Best, Peter
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-- Carlo U. Segre -- Professor of Physics Associate Dean for Special Projects, Graduate College Illinois Institute of Technology Voice: 312.567.3498 Fax: 312.567.3494 segre@agni.phys.iit.edu http://www.iit.edu/~segre
Carlo, (I hope you don't mind me posting this to the list)
I tried your suggestion but the only way I could get the program to produce the correct atom positions, was to delete the old atoms and re-enter them. This is all that is required to fix the error.
O, that's pretty ugly. Reentering the angles seems to be the right thing to do only for the R -3 c space group we were discussing earlier. For P 63 m c it's indeed different. Maybe this is because the former group is a trigonal space group (with a hexagonal nonprimitive unit cell).
What concerns me more is that when I run the command line version of the program with the input file that I showed in my previous email, atoms gives the incorrect results. I can only conclude that there is something funny about the way the atom positions are read in in this case.
That's indeed pretty concerning. Actually for the moment the only safe thing for hexagonal structures seems to be using an old version of atoms (like v2.50) which obviously treats hexagonal structures correctly. Best, Peter -- -------------------------------------------------------------- Peter Pfalzer Universitaet Augsburg Tel: +49-821-598-3215 Lehrstuhl fuer Experimentalphysik II Fax: +49-821-598-3411 Universitaetsstr. 1 D-86135 Augsburg Germany Peter.Pfalzer@physik.uni-augsburg.de --------------------------------------------------------------
participants (2)
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Carlo U. Segre -
Peter Pfalzer