Re: [Ifeffit] X-ray natural circular dichroism by FEFF?
1. X-ray natural circular dichroism by FEFF? (Matthew Marcus) >> >> >> -- >> >> Message: 1 >> Date: Tue, 10 Sep 2013 09:28:44 -0700 >> From: Matthew Marcus >> To: ifeffit@millenia.cars.aps.anl.gov >> Subject: [Ifeffit] X-ray natural circular dichroism by FEFF? >> Message-ID: <522f48bc.8090...@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@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 > To: XAFS Analysis using Ifeffit > Subject: Re: [Ifeffit] X-ray natural circular dichroism by FEFF? > Message-ID: <5230c1d5.9090...@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:0.6 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 >> >> * potphfms 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 >> FMS4.9 >> >> POTENTIALS >> * ipot
[Ifeffit] Using radius in FEFF to determine nanoparticles
Hey all, I started working on modelling nanoparticles with FEFF. 1. Anybody have some useful links about this subject? 2. In 2 reports people were using the radius (i.e. number of atoms used in the calculations) as a measure for the size of the nanoparticles. Further they were discussing the absence of features due to the size. This strikes me odd. I thought that for a) a small SCF radius the feff code might not converge (which cannot give good results), b) when the FMS radius is small - and there are not many scatterers included - the resolution of the calculated XANES spectrum is "bad" and features are broad. I think that has nothing to do with the nanoparticles c) a correct real space feff table of xyz coordinates should include more than just one nanoparticle since the neighboring particles do have an effect on each other - or am I wrong? Thanks. Lisa ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
Re: [Ifeffit] X-ray natural circular dichroism by FEFF?
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:0.6 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 * potphfms 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 FMS4.9 POTENTIALS * ipot z label l_scmt l_fms 0 53 I 3 3 0.01 18 O 2 2 3.00 23 Li 2 2 1.00 3 53 I 3 3 0.99 ATOMS 0.0 0.0 0.00 I0.0 -0.40916-1.44312-0.888471 O1.74338 -1.13161 1.09916-0.888471 O1.81055 1.54125 0.34316-0.888471 O1.81179 0.04130 2.19081 1.852031 O2.86903 -2.03253-0.99669 1.852031 O2.92482 1.99171-1.19491 1.852031 O2.97064 -1.58207-2.53476 0.418752 Li 3.01717 -1.58207 2.63724 0.418752 Li 3.10376 3.16461-0.10326 0.418752 Li 3.19387 0.04130-2.98119 1.852031 O3.50988 2.71415 1.43481 1.852031 O3.58543 -2.75498 1.54559 1.852031 O3.66180 -1.58207-2.53476-2.321752 Li 3.78398 -1.58207 2.63724-2.321752 Li 3.85337 -0.40916 3.72888-0.888471 O3.85504 3.16461-0.10326-2.321752 Li 3.92632 -3.20544-2.08834-0.888471 O3.92751 1.58207 2.53425-2.740503 I4.05410 1.58207 2.53425 2.740503 I4.05410 3.61508-1.64134-0.888471 O4.06843 1.58207-2.63775 2.740503 I4.11959 1.58207-2.63775-2.740503 I4.11959 -3.16461 0.10275 2.740503 I4.18756 -3.16461 0.10275-2.740503 I4.18756 0.04130 2.19081-3.628971 O4.23919 -2.03253-0.99669-3.628971 O4.27715 1.99171-1.19491-3.628971 O4.30861 -1.13161-4.07284-0.888471 O4.31948 -1.58207-2.53476 3.159252 Li 4.34843 -1.58207 2.63724 3.159252 Li 4.40895 3.16461-0.10326 3.159252 Li 4.47284 -3.20544 3.08366-0.888471 O4.53577 4.33752 0.98838-0.888471 O4.53656 0.04130-2.
[Ifeffit] X-ray natural circular dichroism by FEFF?
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:0.6 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 * potphfms 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 FMS4.9 POTENTIALS * ipot z label l_scmt l_fms 0 53 I 3 3 0.01 18 O 2 2 3.00 23 Li 2 2 1.00 3 53 I 3 3 0.99 ATOMS 0.0 0.0 0.00 I0.0 -0.40916-1.44312-0.888471 O1.74338 -1.13161 1.09916-0.888471 O1.81055 1.54125 0.34316-0.888471 O1.81179 0.04130 2.19081 1.852031 O2.86903 -2.03253-0.99669 1.852031 O2.92482 1.99171-1.19491 1.852031 O2.97064 -1.58207-2.53476 0.418752 Li 3.01717 -1.58207 2.63724 0.418752 Li 3.10376 3.16461-0.10326 0.418752 Li 3.19387 0.04130-2.98119 1.852031 O3.50988 2.71415 1.43481 1.852031 O3.58543 -2.75498 1.54559 1.852031 O3.66180 -1.58207-2.53476-2.321752 Li 3.78398 -1.58207 2.63724-2.321752 Li 3.85337 -0.40916 3.72888-0.888471 O3.85504 3.16461-0.10326-2.321752 Li 3.92632 -3.20544-2.08834-0.888471 O3.92751 1.58207 2.53425-2.740503 I4.05410 1.58207 2.53425 2.740503 I4.05410 3.61508-1.64134-0.888471 O4.06843 1.58207-2.63775 2.740503 I4.11959 1.58207-2.63775-2.740503 I4.11959 -3.16461 0.10275 2.740503 I4.18756 -3.16461 0.10275-2.740503 I4.18756 0.04130 2.19081-3.628971 O4.23919 -2.03253-0.99669-3.628971 O4.27715 1.99171-1.19491-3.628971 O4.30861 -1.13161-4.07284-0.888471 O4.31948 -1.58207-2.53476 3.159252 Li 4.34843 -1.58207 2.63724 3.159252 Li 4.40895 3.16461-0.10326 3.159252 Li 4.47284 -3.20544 3.08366-0.888471 O4.53577 4.33752 0.98838-0.888471 O4.53656 0.04130-2.98119-3.628971 O4.69666 2.71415 1.43481-3.628971 O4.75339 -2.75498 1.54559-3.628971 O4.81125
Re: [Ifeffit] Using radius in FEFF to determine nanoparticles
Lisa, The number of papers using FEFF to model nanoparticles is in the thousands. Starting with FEFF8, most XANES features can be reliably modeled. Look for papers by J.Kas and others from J.Rehr group for details. Neighboring nanoparticles do not contribute, one reason being that XAS is dominated by the interior of the particle, and there are many other reasons, but that one is the most important. Too few atoms on the first particle will see the atoms on the second particle to make contribution to average XAS. These contributions will be also strongly disordered and tend to cancel each other. Anatoly Sent from my iPad On Sep 11, 2013, at 10:57 AM, "Lisa Bovenkamp" wrote: > Hey all, > > I started working on modelling nanoparticles with FEFF. > 1. Anybody have some useful links about this subject? > > 2. In 2 reports people were using the radius (i.e. number of atoms > used in the calculations) as a measure for the size of the nanoparticles. > Further they were discussing the absence of features due to the > size. > This strikes me odd. I thought that for > a) a small SCF radius the feff code might not converge (which cannot give > good results), > b) when the FMS radius is small - and there are not many scatterers included > - > the resolution of the calculated XANES spectrum is "bad" and features are > broad. > I think that has nothing to do with the nanoparticles > c) a correct real space feff table of xyz coordinates should include more > than just one > nanoparticle since the neighboring particles do have an effect on each other > - or am I wrong? > > Thanks. > Lisa > > > > > ___ > Ifeffit mailing list > Ifeffit@millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > ___ Ifeffit mailing list Ifeffit@millenia.cars.aps.anl.gov http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit
