Re: [Ifeffit] FEFF input files

4 Jul 2011

      Hi Zohair,

Thanks for the suggestion.

Part of me is pleased by this, while the other part of me asked the question in the first place. Please let me explain.

I am pleased because I did actually go through exactly the exercise you suggest prior to my post. However, a few aspects made me uncertain about this process. Firstly, I found that my choice of "starting structure" (Mn_2O_3) was fairly random, i.e. there are others in the database with the right format ('element'_2O_3), and Mn2O3 and Gd2O3 are not the same space group. As a consequence I did not feel comfortable with simply pulling across the X,Y,Z coordinates from Mn2O3.

Anna's more recent e-mail (thanks Anna!) seems to bring me closer to an answer I can believe in, although the database she refers to has two Gd2O3 entries, each giving two quite different answers in terms of paths.

Thanks again for your advice.

Cheers,

Bernt

From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Zohair.Hussain@csiro.au
Sent: Monday, 4 July 2011 5:55 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: Re: [Ifeffit] FEFF input files

Hi Bernt,

Here's my take on it. It's based on the assumption that Gd2O3 structure is similar to Mn2O3. Hence, I've modified the Mn2O3 file to replace Mn with Gd and have the larger a of 10.82.

Zohair

 * This feff6 input file was generated by WebAtoms 1.8 (Atoms 3.0beta10)

 * Atoms written by and copyright (c) Bruce Ravel, 1998-2001

 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *

 *   total mu*x=1:     3.99 microns,  unit edge step:    13.05 microns

 *   specific gravity =  7.604

 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *

 *   Normalization correction:    0.00062 ang^2

 * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *

 * -----------------------------------------------------------------

 * The following crystallographic data were used:

 *

 * title       name:     Gd2O3

 * title       formula:  Gd2O3

 * title       sites:    Gd1--2,O1

 * title       refer1:   Wyckoff vol 2, V, p 2-4

 * title       schoen:   D_3d^3

 * space = I a -3

 * a =   10.820 b =      10.820 c =      10.820

 * alpha =      90.0   beta =   90.0   gamma =  90.0

 * core =      Gd1     edge =  L3

 * atoms

 * ! elem   x          y          z       tag        occ

 *   Gd    0.25000    0.25000    0.25000  Gd1           1.00000

 *   Gd   -0.03470    0.00000    0.25000  Gd2           1.00000

 *   O     0.37800    0.16700    0.39700  O1            1.00000

 * -----------------------------------------------------------------

 TITLE name:     Gd2O3

 TITLE formula:  Gd2O3

 TITLE sites:    Gd1--2,O1

 TITLE refer1:   Wyckoff vol 2, V, p 2-4

 TITLE schoen:   D_3d^3

 HOLE 4   1.0   *  Gd L3 edge  (7243.0 eV), second number is S0^2

 *         mphase,mpath,mfeff,mchi

 CONTROL   1      1     1     1

 PRINT     1      0     0     0

 RMAX        6.0

 *CRITERIA     curved   plane

 *DEBYE        temp     debye-temp

 NLEG         4

 POTENTIALS

 *    ipot   Z  element

	0   64   Gd

	1   64   Gd

	2    8   O

 ATOMS                          * this list contains 49 atoms

 *   x          y          z      ipot  tag              distance

    0.00000    0.00000    0.00000  0 Gd1             0.00000

   -1.59054   -1.38496    0.89806  2 O1_1            2.29226

   -0.89806    1.59054    1.38496  2 O1_1            2.29226

    1.38496   -0.89806    1.59054  2 O1_1            2.29226

    1.59054    1.38496   -0.89806  2 O1_1            2.29226

    0.89806   -1.59054   -1.38496  2 O1_1            2.29226

   -1.38496    0.89806   -1.59054  2 O1_1            2.29226

   -2.32955    2.70500    0.00000  1 Gd2_1           3.56985

    2.32955   -2.70500    0.00000  1 Gd2_1           3.56985

   -2.70500    0.00000    2.32955  1 Gd2_1           3.56985

    0.00000   -2.32955    2.70500  1 Gd2_1           3.56985

    2.70500    0.00000   -2.32955  1 Gd2_1           3.56985

    0.00000    2.32955   -2.70500  1 Gd2_1           3.56985

    3.08045    2.70500    0.00000  1 Gd2_2           4.09954

   -3.08045   -2.70500    0.00000  1 Gd2_2           4.09954

    0.00000    3.08045    2.70500  1 Gd2_2           4.09954

    2.70500    0.00000    3.08045  1 Gd2_2           4.09954

    0.00000   -3.08045   -2.70500  1 Gd2_2           4.09954

   -2.70500    0.00000   -3.08045  1 Gd2_2           4.09954

   -3.81946    1.38496    0.89806  2 O1_2            4.16088

    0.89806   -3.81946    1.38496  2 O1_2            4.16088

   -1.38496   -0.89806    3.81946  2 O1_2            4.16088

    3.81946   -1.38496   -0.89806  2 O1_2            4.16088

   -0.89806    3.81946   -1.38496  2 O1_2            4.16088

    1.38496    0.89806   -3.81946  2 O1_2            4.16088

    1.59054    4.02504    0.89806  2 O1_3            4.42010

    4.02504    0.89806    1.59054  2 O1_3            4.42010

    0.89806    1.59054    4.02504  2 O1_3            4.42010

   -1.59054   -4.02504   -0.89806  2 O1_3            4.42010

   -4.02504   -0.89806   -1.59054  2 O1_3            4.42010

   -0.89806   -1.59054   -4.02504  2 O1_3            4.42010

   -4.51194   -1.59054    1.38496  2 O1_4            4.98052

   -1.38496    4.51194    1.59054  2 O1_4            4.98052

    1.59054   -1.38496    4.51194  2 O1_4            4.98052

    4.51194    1.59054   -1.38496  2 O1_4            4.98052

    1.38496   -4.51194   -1.59054  2 O1_4            4.98052

   -1.59054    1.38496   -4.51194  2 O1_4            4.98052

    5.41000    0.00000    0.00000  1 Gd1_1           5.41000

   -5.41000    0.00000    0.00000  1 Gd1_1           5.41000

    0.00000    5.41000    0.00000  1 Gd1_1           5.41000

    0.00000   -5.41000    0.00000  1 Gd1_1           5.41000

    0.00000    0.00000    5.41000  1 Gd1_1           5.41000

    0.00000    0.00000   -5.41000  1 Gd1_1           5.41000

    3.81946   -4.02504    0.89806  2 O1_5            5.62101

   -4.02504    0.89806    3.81946  2 O1_5            5.62101

   -0.89806   -3.81946    4.02504  2 O1_5            5.62101

   -3.81946    4.02504   -0.89806  2 O1_5            5.62101

    4.02504   -0.89806   -3.81946  2 O1_5            5.62101

    0.89806    3.81946   -4.02504  2 O1_5            5.62101

 END

From: ifeffit-bounces@millenia.cars.aps.anl.gov [mailto:ifeffit-bounces@millenia.cars.aps.anl.gov] On Behalf Of Bernt Johannessen
Sent: Monday, 4 July 2011 5:07 PM
To: ifeffit@millenia.cars.aps.anl.gov
Subject: [Ifeffit] FEFF input files

Dear All,

I am looking at using Artemis ("Theory"; "New Atoms page") to create FEFF input files for Gd and Gd2O3. I believe I have got the Gd parameters right:

Space group 194
a=b=3.636,c=5.7826
alpha=beta=90,gamma=120
Gd: X=Y=Z=0

And it does give me reasonable paths in the end to work with (see below FEFF.inp file)

The Gd2O3 is trickier (space group 206, a=b=c=10.8(?), alpha=beta=gamma=0):

How do I determine the X,Y,Z coordinates for the relevant atoms?

Regards,

Bernt

Gd FEFF input file:
* This feff6 input file was generated by Artemis 0.8.012
* Atoms written by and copyright (c) Bruce Ravel, 1998-2001

* -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
 *   total mu*x=1:     3.36 microns,  unit edge step:     5.46 microns
*   specific gravity =  7.888
* -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
 *   Normalization correction:    0.00062 ang^2
* -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *

* -----------------------------------------------------------------
* The following crystallographic data were used:
*
* title   ...
* space = P 63/m m c
* a =       3.6360 b =            3.6360 c =            5.78260
* alpha =             90.0       beta =   90.0       gamma =             120.0
* core =               Gd1        edge =  L3
* atoms
* ! elem   x          y          z       tag        occ
*   Gd    0.00000    0.00000    0.00000  Gd1           1.00000
* -----------------------------------------------------------------

TITLE ...

HOLE 4   1.0   *  Gd L3 edge  (7243.0 eV), second number is S0^2

*         mphase,mpath,mfeff,mchi
CONTROL   1      1     1     1
PRINT     1      0     0     0

RMAX        6.0

*CRITERIA     curved   plane
*DEBYE        temp     debye-temp
NLEG         4

POTENTIALS
*    ipot   Z  element
	0   64   Gd
	1   64   Gd

ATOMS                          * this list contains 23 atoms
*   x          y          z      ipot  tag              distance
    0.00000    0.00000    0.00000  0 Gd1             0.00000
    0.00000    0.00000    2.89130  1 Gd1_1           2.89130
    0.00000    0.00000   -2.89130  1 Gd1_1           2.89130
    3.14887    1.81800    0.00000  1 Gd1_2           3.63600
   -3.14887    1.81800    0.00000  1 Gd1_2           3.63600
    0.00000    3.63600    0.00000  1 Gd1_2           3.63600
    3.14887   -1.81800    0.00000  1 Gd1_2           3.63600
   -3.14887   -1.81800    0.00000  1 Gd1_2           3.63600
    0.00000   -3.63600    0.00000  1 Gd1_2           3.63600
    3.14887    1.81800    2.89130  1 Gd1_3           4.64544
   -3.14887    1.81800    2.89130  1 Gd1_3           4.64544
    0.00000    3.63600    2.89130  1 Gd1_3           4.64544
    3.14887   -1.81800    2.89130  1 Gd1_3           4.64544
   -3.14887   -1.81800    2.89130  1 Gd1_3           4.64544
    0.00000   -3.63600    2.89130  1 Gd1_3           4.64544
    3.14887    1.81800   -2.89130  1 Gd1_3           4.64544
   -3.14887    1.81800   -2.89130  1 Gd1_3           4.64544
    0.00000    3.63600   -2.89130  1 Gd1_3           4.64544
    3.14887   -1.81800   -2.89130  1 Gd1_3           4.64544
   -3.14887   -1.81800   -2.89130  1 Gd1_3           4.64544
    0.00000   -3.63600   -2.89130  1 Gd1_3           4.64544
    0.00000    0.00000    5.78260  1 Gd1_4           5.78260
    0.00000    0.00000   -5.78260  1 Gd1_4           5.78260
END

[cid:image001.gif@01CC3A9A.FEC241A0]
Bernt Johannessen | Scientist - XAS | Australian Synchrotron
p: (03) 8540 4240 | f: (03) 8540 4200
bernt.johannessen@synchrotron.org.aumailto:bernt.johannessen@synchrotron.org.au | www.synchrotron.org.au
800 Blackburn Road, Clayton, Victoria 3168

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<br>This message and any attachments may contain proprietary or confidential information. If you are not the intended recipient or you received the message in error, you must not use, copy or distribute the message. Please notify the sender immediately and destroy the original message. Thank you.