[Ifeffit] X-ray natural circular dichroism by FEFF?
Joshua Kas
joshua.j.kas at gmail.com
Wed Sep 11 15:02:27 CDT 2013
Hi Matthew,
XNCD is due to dipole-quadrupole interference terms. See for example,
Ankudinov, Phys. Rev. B 62, 2437–2445 (2000)
Cheers,
Josh
On Wed, Sep 11, 2013 at 12:18 PM,
<ifeffit-request at millenia.cars.aps.anl.gov> wrote:
> Send Ifeffit mailing list submissions to
> ifeffit at millenia.cars.aps.anl.gov
>
> To subscribe or unsubscribe via the World Wide Web, visit
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
> or, via email, send a message with subject or body 'help' to
> ifeffit-request at millenia.cars.aps.anl.gov
>
> You can reach the person managing the list at
> ifeffit-owner at millenia.cars.aps.anl.gov
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Ifeffit digest..."
>
>
> Today's Topics:
>
> 1. X-ray natural circular dichroism by FEFF? (Joshua Kas)
> 2. Re: X-ray natural circular dichroism by FEFF? (Matthew Marcus)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Wed, 11 Sep 2013 10:59:37 -0700
> From: Joshua Kas <joshua.j.kas at gmail.com>
> To: ifeffit at millenia.cars.aps.anl.gov
> Subject: [Ifeffit] X-ray natural circular dichroism by FEFF?
> Message-ID:
> <CAHuhYR=X20USCUMtorXtvTcY-yoguDcbEm+LTMrw1y2P2m_G=w at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Matthew,
> Sorry it took a while to answer your questions. No one has used the
> XNCD features of FEFF for quite some time, and the example files that
> were lying around did not run correctly. However, I have now
> reproduced the output from one for the LiIO3 example. Please see the
> input below. The main things that are essential are:
> 1. The setting
> MULTIPOLE 2
> which turns on quadrupole effects.
> 2. The XNCD card.
> 3. The ELLIPTICITY card to tell the program the direction of x-ray
> propagation, i.e.,
> ELLIPTICITY elipticity kx ky kz
> for example, circular polarization in the z direction is specified by
> ELLIPTICITY 1 0 0 1
> If you don't specify the ELLIPTICITY, and the XNCD card is
> specified, the program will
> assume circularly polarized light traveling in the z direction.
>
> I am also attaching the results that I get from FEFF9. The xncd signal
> is in column 6.
>
> Cheers,
> Josh Kas
>
> * Example feff input file for XNCD of LiIO3
> * This feff.inp file generated by ATOMS, version 2.46c
> * ATOMS written by Bruce Ravel and copyright of The Univ. of Washington, 1994
>
> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
> * total mu = 112.7 cm^-1, delta mu = 92.0 cm^-1
> * specific gravity = 4.488, cluster contains 547 atoms.
> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
> * mcmaster corrections: 0.00014 ang^2 and 0.403E-07 ang^4
> * self-abs. corrections: amplitude factor = 4.652
> * 0.00011 ang^2 and 0.252E-07 ang^4
> * i0 corrections: 0.00006 ang^2 and 0.269E-07 ang^4
> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
> * sum of corrections: 0.00031 ang^2 and 0.923E-07 ang^4
> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
>
> TITLE LiIO3
>
> HOLE 4 1.0 I L3 edge, second number is S0^2
> SCF 4.0
>
> * pot ph fms paths genfmt ff2chi
> CONTROL 1 1 1 1 1 1
>
>
> XANES 5.5 0.05 0.5
> * absorption with averaging over left and right circular polarizations
> *POLARIZATION 1 0 0
> MULTIPOLE 2
> ELLIPTICITY 1 0 0 1
>
> * XNCD calculations; comment out for above average absorption
> XNCD
>
> EXCHANGE 0 1 0.0 2
> RPATH 0.1
>
> * 41-atom cluster
> FMS 4.9
>
> POTENTIALS
> * ipot z label l_scmt l_fms
> 0 53 I 3 3 0.01
> 1 8 O 2 2 3.00
> 2 3 Li 2 2 1.00
> 3 53 I 3 3 0.99
>
> ATOMS
> 0.00000 0.00000 0.00000 0 I 0.00000
> -0.40916 -1.44312 -0.88847 1 O 1.74338
> -1.13161 1.09916 -0.88847 1 O 1.81055
> 1.54125 0.34316 -0.88847 1 O 1.81179
> 0.04130 2.19081 1.85203 1 O 2.86903
> -2.03253 -0.99669 1.85203 1 O 2.92482
> 1.99171 -1.19491 1.85203 1 O 2.97064
> -1.58207 -2.53476 0.41875 2 Li 3.01717
> -1.58207 2.63724 0.41875 2 Li 3.10376
> 3.16461 -0.10326 0.41875 2 Li 3.19387
> 0.04130 -2.98119 1.85203 1 O 3.50988
> 2.71415 1.43481 1.85203 1 O 3.58543
> -2.75498 1.54559 1.85203 1 O 3.66180
> -1.58207 -2.53476 -2.32175 2 Li 3.78398
> -1.58207 2.63724 -2.32175 2 Li 3.85337
> -0.40916 3.72888 -0.88847 1 O 3.85504
> 3.16461 -0.10326 -2.32175 2 Li 3.92632
> -3.20544 -2.08834 -0.88847 1 O 3.92751
> 1.58207 2.53425 -2.74050 3 I 4.05410
> 1.58207 2.53425 2.74050 3 I 4.05410
> 3.61508 -1.64134 -0.88847 1 O 4.06843
> 1.58207 -2.63775 2.74050 3 I 4.11959
> 1.58207 -2.63775 -2.74050 3 I 4.11959
> -3.16461 0.10275 2.74050 3 I 4.18756
> -3.16461 0.10275 -2.74050 3 I 4.18756
> 0.04130 2.19081 -3.62897 1 O 4.23919
> -2.03253 -0.99669 -3.62897 1 O 4.27715
> 1.99171 -1.19491 -3.62897 1 O 4.30861
> -1.13161 -4.07284 -0.88847 1 O 4.31948
> -1.58207 -2.53476 3.15925 2 Li 4.34843
> -1.58207 2.63724 3.15925 2 Li 4.40895
> 3.16461 -0.10326 3.15925 2 Li 4.47284
> -3.20544 3.08366 -0.88847 1 O 4.53577
> 4.33752 0.98838 -0.88847 1 O 4.53656
> 0.04130 -2.98119 -3.62897 1 O 4.69666
> 2.71415 1.43481 -3.62897 1 O 4.75339
> -2.75498 1.54559 -3.62897 1 O 4.81125
> 1.99171 3.97709 1.85203 1 O 4.81811
> -0.40916 -1.44312 4.59253 1 O 4.83129
> -1.13161 1.09916 4.59253 1 O 4.85593
> 1.54125 0.34316 4.59253 1 O 4.85639
> -2.75498 -3.62641 1.85203 1 O 4.91638
> 2.71415 -3.73719 1.85203 1 O 4.97627
> -2.03253 4.17531 1.85203 1 O 4.99944
> -4.70539 -0.24069 1.85203 1 O 5.06247
> 3.61508 3.53066 -0.88847 1 O 5.13066
> 1.54125 -4.82884 -0.88847 1 O 5.14611
> 4.78798 -0.54969 1.85203 1 O 5.16304
> 0.00000 -5.17200 0.00000 3 I 5.17200
> 0.00000 5.17200 0.00000 3 I 5.17200
> -4.74669 -2.43150 0.00000 3 I 5.33322
> 4.74669 2.43150 0.00000 3 I 5.33322
> -5.15585 1.29738 -0.88847 1 O 5.39030
> 0.00000 0.00000 5.48100 3 I 5.48100
> 0.00000 0.00000 -5.48100 3 I 5.48100
> 4.74669 -2.74050 0.00000 3 I 5.48100
> -4.74669 2.74050 0.00000 3 I 5.48100
> 1.99171 3.97709 -3.62897 1 O 5.74052
> 1.54125 5.51516 -0.88847 1 O 5.79499
> -2.75498 -3.62641 -3.62897 1 O 5.82324
> 2.71415 -3.73719 -3.62897 1 O 5.87390
> -1.58207 -2.53476 -5.06225 2 Li 5.87830
> -2.03253 4.17531 -3.62897 1 O 5.89354
> -1.58207 2.63724 -5.06225 2 Li 5.92320
> -0.40916 3.72888 4.59253 1 O 5.92987
> -4.70539 -0.24069 -3.62897 1 O 5.94710
> 3.16461 -0.10326 -5.06225 2 Li 5.97092
> -3.20544 -2.08834 4.59253 1 O 5.97723
> 3.16461 5.06874 0.41875 2 Li 5.99018
> END
>
> On Tue, Sep 10, 2013 at 10:00 AM,
> <ifeffit-request at millenia.cars.aps.anl.gov> wrote:
>> Send Ifeffit mailing list submissions to
>> ifeffit at millenia.cars.aps.anl.gov
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>> or, via email, send a message with subject or body 'help' to
>> ifeffit-request at millenia.cars.aps.anl.gov
>>
>> You can reach the person managing the list at
>> ifeffit-owner at millenia.cars.aps.anl.gov
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of Ifeffit digest..."
>>
>>
>> Today's Topics:
>>
>> 1. X-ray natural circular dichroism by FEFF? (Matthew Marcus)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Tue, 10 Sep 2013 09:28:44 -0700
>> From: Matthew Marcus <mamarcus at lbl.gov>
>> To: ifeffit at millenia.cars.aps.anl.gov
>> Subject: [Ifeffit] X-ray natural circular dichroism by FEFF?
>> Message-ID: <522F48BC.8090402 at lbl.gov>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>
>> Can FEFF calculate X-ray natural circular dichroism, which is the XCD that comes from structural chirality and not
>> magnetism? I suppose I could simply try it, putting in coordinates for some simple molecule, but I'd like to know
>> if any results would be meaningful.
>> mam
>>
>>
>> ------------------------------
>>
>> _______________________________________________
>> Ifeffit mailing list
>> Ifeffit at millenia.cars.aps.anl.gov
>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>
>>
>> End of Ifeffit Digest, Vol 127, Issue 9
>> ***************************************
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: xmu.dat
> Type: application/octet-stream
> Size: 8058 bytes
> Desc: not available
> URL: <http://millenia.cars.aps.anl.gov/pipermail/ifeffit/attachments/20130911/9fb15960/attachment-0001.obj>
>
> ------------------------------
>
> Message: 2
> Date: Wed, 11 Sep 2013 12:17:41 -0700
> From: Matthew Marcus <mamarcus at lbl.gov>
> To: XAFS Analysis using Ifeffit <ifeffit at millenia.cars.aps.anl.gov>
> Subject: Re: [Ifeffit] X-ray natural circular dichroism by FEFF?
> Message-ID: <5230C1D5.9090200 at lbl.gov>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Thanks. So XNCD is an effect of the quadrupole terms?
> mam
>
> On 9/11/2013 10:59 AM, Joshua Kas wrote:
>> Hi Matthew,
>> Sorry it took a while to answer your questions. No one has used the
>> XNCD features of FEFF for quite some time, and the example files that
>> were lying around did not run correctly. However, I have now
>> reproduced the output from one for the LiIO3 example. Please see the
>> input below. The main things that are essential are:
>> 1. The setting
>> MULTIPOLE 2
>> which turns on quadrupole effects.
>> 2. The XNCD card.
>> 3. The ELLIPTICITY card to tell the program the direction of x-ray
>> propagation, i.e.,
>> ELLIPTICITY elipticity kx ky kz
>> for example, circular polarization in the z direction is specified by
>> ELLIPTICITY 1 0 0 1
>> If you don't specify the ELLIPTICITY, and the XNCD card is
>> specified, the program will
>> assume circularly polarized light traveling in the z direction.
>>
>> I am also attaching the results that I get from FEFF9. The xncd signal
>> is in column 6.
>>
>> Cheers,
>> Josh Kas
>>
>> * Example feff input file for XNCD of LiIO3
>> * This feff.inp file generated by ATOMS, version 2.46c
>> * ATOMS written by Bruce Ravel and copyright of The Univ. of Washington, 1994
>>
>> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
>> * total mu = 112.7 cm^-1, delta mu = 92.0 cm^-1
>> * specific gravity = 4.488, cluster contains 547 atoms.
>> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
>> * mcmaster corrections: 0.00014 ang^2 and 0.403E-07 ang^4
>> * self-abs. corrections: amplitude factor = 4.652
>> * 0.00011 ang^2 and 0.252E-07 ang^4
>> * i0 corrections: 0.00006 ang^2 and 0.269E-07 ang^4
>> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
>> * sum of corrections: 0.00031 ang^2 and 0.923E-07 ang^4
>> * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- * -- *
>>
>> TITLE LiIO3
>>
>> HOLE 4 1.0 I L3 edge, second number is S0^2
>> SCF 4.0
>>
>> * pot ph fms paths genfmt ff2chi
>> CONTROL 1 1 1 1 1 1
>>
>>
>> XANES 5.5 0.05 0.5
>> * absorption with averaging over left and right circular polarizations
>> *POLARIZATION 1 0 0
>> MULTIPOLE 2
>> ELLIPTICITY 1 0 0 1
>>
>> * XNCD calculations; comment out for above average absorption
>> XNCD
>>
>> EXCHANGE 0 1 0.0 2
>> RPATH 0.1
>>
>> * 41-atom cluster
>> FMS 4.9
>>
>> POTENTIALS
>> * ipot z label l_scmt l_fms
>> 0 53 I 3 3 0.01
>> 1 8 O 2 2 3.00
>> 2 3 Li 2 2 1.00
>> 3 53 I 3 3 0.99
>>
>> ATOMS
>> 0.00000 0.00000 0.00000 0 I 0.00000
>> -0.40916 -1.44312 -0.88847 1 O 1.74338
>> -1.13161 1.09916 -0.88847 1 O 1.81055
>> 1.54125 0.34316 -0.88847 1 O 1.81179
>> 0.04130 2.19081 1.85203 1 O 2.86903
>> -2.03253 -0.99669 1.85203 1 O 2.92482
>> 1.99171 -1.19491 1.85203 1 O 2.97064
>> -1.58207 -2.53476 0.41875 2 Li 3.01717
>> -1.58207 2.63724 0.41875 2 Li 3.10376
>> 3.16461 -0.10326 0.41875 2 Li 3.19387
>> 0.04130 -2.98119 1.85203 1 O 3.50988
>> 2.71415 1.43481 1.85203 1 O 3.58543
>> -2.75498 1.54559 1.85203 1 O 3.66180
>> -1.58207 -2.53476 -2.32175 2 Li 3.78398
>> -1.58207 2.63724 -2.32175 2 Li 3.85337
>> -0.40916 3.72888 -0.88847 1 O 3.85504
>> 3.16461 -0.10326 -2.32175 2 Li 3.92632
>> -3.20544 -2.08834 -0.88847 1 O 3.92751
>> 1.58207 2.53425 -2.74050 3 I 4.05410
>> 1.58207 2.53425 2.74050 3 I 4.05410
>> 3.61508 -1.64134 -0.88847 1 O 4.06843
>> 1.58207 -2.63775 2.74050 3 I 4.11959
>> 1.58207 -2.63775 -2.74050 3 I 4.11959
>> -3.16461 0.10275 2.74050 3 I 4.18756
>> -3.16461 0.10275 -2.74050 3 I 4.18756
>> 0.04130 2.19081 -3.62897 1 O 4.23919
>> -2.03253 -0.99669 -3.62897 1 O 4.27715
>> 1.99171 -1.19491 -3.62897 1 O 4.30861
>> -1.13161 -4.07284 -0.88847 1 O 4.31948
>> -1.58207 -2.53476 3.15925 2 Li 4.34843
>> -1.58207 2.63724 3.15925 2 Li 4.40895
>> 3.16461 -0.10326 3.15925 2 Li 4.47284
>> -3.20544 3.08366 -0.88847 1 O 4.53577
>> 4.33752 0.98838 -0.88847 1 O 4.53656
>> 0.04130 -2.98119 -3.62897 1 O 4.69666
>> 2.71415 1.43481 -3.62897 1 O 4.75339
>> -2.75498 1.54559 -3.62897 1 O 4.81125
>> 1.99171 3.97709 1.85203 1 O 4.81811
>> -0.40916 -1.44312 4.59253 1 O 4.83129
>> -1.13161 1.09916 4.59253 1 O 4.85593
>> 1.54125 0.34316 4.59253 1 O 4.85639
>> -2.75498 -3.62641 1.85203 1 O 4.91638
>> 2.71415 -3.73719 1.85203 1 O 4.97627
>> -2.03253 4.17531 1.85203 1 O 4.99944
>> -4.70539 -0.24069 1.85203 1 O 5.06247
>> 3.61508 3.53066 -0.88847 1 O 5.13066
>> 1.54125 -4.82884 -0.88847 1 O 5.14611
>> 4.78798 -0.54969 1.85203 1 O 5.16304
>> 0.00000 -5.17200 0.00000 3 I 5.17200
>> 0.00000 5.17200 0.00000 3 I 5.17200
>> -4.74669 -2.43150 0.00000 3 I 5.33322
>> 4.74669 2.43150 0.00000 3 I 5.33322
>> -5.15585 1.29738 -0.88847 1 O 5.39030
>> 0.00000 0.00000 5.48100 3 I 5.48100
>> 0.00000 0.00000 -5.48100 3 I 5.48100
>> 4.74669 -2.74050 0.00000 3 I 5.48100
>> -4.74669 2.74050 0.00000 3 I 5.48100
>> 1.99171 3.97709 -3.62897 1 O 5.74052
>> 1.54125 5.51516 -0.88847 1 O 5.79499
>> -2.75498 -3.62641 -3.62897 1 O 5.82324
>> 2.71415 -3.73719 -3.62897 1 O 5.87390
>> -1.58207 -2.53476 -5.06225 2 Li 5.87830
>> -2.03253 4.17531 -3.62897 1 O 5.89354
>> -1.58207 2.63724 -5.06225 2 Li 5.92320
>> -0.40916 3.72888 4.59253 1 O 5.92987
>> -4.70539 -0.24069 -3.62897 1 O 5.94710
>> 3.16461 -0.10326 -5.06225 2 Li 5.97092
>> -3.20544 -2.08834 4.59253 1 O 5.97723
>> 3.16461 5.06874 0.41875 2 Li 5.99018
>> END
>>
>> On Tue, Sep 10, 2013 at 10:00 AM,
>> <ifeffit-request at millenia.cars.aps.anl.gov> wrote:
>>> Send Ifeffit mailing list submissions to
>>> ifeffit at millenia.cars.aps.anl.gov
>>>
>>> To subscribe or unsubscribe via the World Wide Web, visit
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>> or, via email, send a message with subject or body 'help' to
>>> ifeffit-request at millenia.cars.aps.anl.gov
>>>
>>> You can reach the person managing the list at
>>> ifeffit-owner at millenia.cars.aps.anl.gov
>>>
>>> When replying, please edit your Subject line so it is more specific
>>> than "Re: Contents of Ifeffit digest..."
>>>
>>>
>>> Today's Topics:
>>>
>>> 1. X-ray natural circular dichroism by FEFF? (Matthew Marcus)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Tue, 10 Sep 2013 09:28:44 -0700
>>> From: Matthew Marcus <mamarcus at lbl.gov>
>>> To: ifeffit at millenia.cars.aps.anl.gov
>>> Subject: [Ifeffit] X-ray natural circular dichroism by FEFF?
>>> Message-ID: <522F48BC.8090402 at lbl.gov>
>>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>>>
>>> Can FEFF calculate X-ray natural circular dichroism, which is the XCD that comes from structural chirality and not
>>> magnetism? I suppose I could simply try it, putting in coordinates for some simple molecule, but I'd like to know
>>> if any results would be meaningful.
>>> mam
>>>
>>>
>>> ------------------------------
>>>
>>> _______________________________________________
>>> Ifeffit mailing list
>>> Ifeffit at millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>>>
>>>
>>> End of Ifeffit Digest, Vol 127, Issue 9
>>> ***************************************
>>>
>>>
>>> _______________________________________________
>>> Ifeffit mailing list
>>> Ifeffit at millenia.cars.aps.anl.gov
>>> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> ------------------------------
>
> _______________________________________________
> Ifeffit mailing list
> Ifeffit at millenia.cars.aps.anl.gov
> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
>
>
> End of Ifeffit Digest, Vol 127, Issue 11
> ****************************************
More information about the Ifeffit
mailing list