- Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Installation problems Ubuntu 12.04
by Denis Testemale 12 Sep '13

12 Sep '13

Dear list. I'm in a similar configuration (Ubuntu 13.04) and tried recently to upgrade Demeter (0.9.18). This is a short report. I ran in the exact same problems than David reported. I installed manually libsoap as suggested and it worked. I still have some fail messages during the building process though. See the attachments: - one is the output of the ./Build test command - one image is the corresponding screen snapshot which is a bit more verbose about the error. I was wondering if it could generate errors later when I use the softwares even if they seem to install fine. Another minor point is that the link about the Demeter homepage (in the "About" page) sent me to a page with an error (see 3rd attachment). Cheers denis Le 07/09/2013 19:00, ifeffit-request(a)millenia.cars.aps.anl.gov a écrit : > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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. Re: Installation problems Ubuntu 12.04 (David Eveborn) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 6 Sep 2013 23:56:45 +0200 > From: David Eveborn <david.eveborn(a)gmail.com> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Installation problems Ubuntu 12.04 > Message-ID: > <CAGs9LMFwe12oyk3VDaxBVsR71tOdfCntJAaOymmo+sqffHMU_w(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Bruce and Ivan > > By following your advice I was able to install the demeter package! > Installing libsoap-lite-perl by apt-get helped me out. Thank you! Look > forward to explore the demeter API now! > > Kind regards > > David >

3 2

Using radius in FEFF to determine nanoparticles
by Lisa Bovenkamp 12 Sep '13

12 Sep '13

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

3 2

Upon updating Demeter on 9/4, pluck results in both Artemis and Athena not responding
by Heidi Jensen 12 Sep '13

12 Sep '13

I wanted to see if anyone can help me with a problem that I am experiencing (log files below). I am running Demeter on Windows 7. I updated the Demeter package last week using the updater package (0.9.18.2) and have had issues when attempting to pluck points from plots since then. I am confident that at the time of update, I had the current version of the installer package. The window that usually pops up when you click on the pluck boxes does not come up and both Artemis and Athena stop responding for about 30 seconds and then return to normal function, but without allowing me to select any points in the plotting window. This does not crash either program completely. In Artemis, I tried to use the pluck command to select the fitting range. In Athena, I tried it with both selecting points for the k-range of the Forward Fourier transformation and in the Deglitching and truncation window. I think that I may try to uninstall the Demeter package and start over and see what that does. Thanks for your help. Heidi Jensen Artemis: Started at 2013-09-05T16:05:49 Win7Professional (64-bit) Service Pack 1 Service Pack 16176012102561 PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\Program Files\Intel\DMIX;C:\Program Files (x86)\PharosSystems\Core;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\Program Files (x86)\QuickTime\QTSystem\ perl version: v5.12.3 @INC: C:/strawberry/perl/site/lib C:/strawberry/perl/vendor/lib C:/strawberry/perl/lib . Athena: Started at 2013-09-10T15:17:12 Win7Professional (64-bit) Service Pack 1 Service Pack 16176012102561 PATH: C:\Windows\system32;C:\Windows;C:\Windows\System32\Wbem;C:\Windows\System32\WindowsPowerShell\v1.0\;C:\Program Files\Intel\WiFi\bin\;C:\Program Files\Common Files\Intel\WirelessCommon\;C:\Program Files\Intel\DMIX;C:\Program Files (x86)\PharosSystems\Core;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\Program Files (x86)\QuickTime\QTSystem\ perl version: v5.12.3 @INC: C:/strawberry/perl/site/lib C:/strawberry/perl/vendor/lib C:/strawberry/perl/lib .

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Re: [Ifeffit] X-ray natural circular dichroism by FEFF?
by Joshua Kas 11 Sep '13

11 Sep '13

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(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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(a)gmail.com> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] X-ray natural circular dichroism by FEFF? > Message-ID: > <CAHuhYR=X20USCUMtorXtvTcY-yoguDcbEm+LTMrw1y2P2m_G=w(a)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(a)millenia.cars.aps.anl.gov> wrote: >> Send Ifeffit mailing list submissions to >> ifeffit(a)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(a)millenia.cars.aps.anl.gov >> >> You can reach the person managing the list at >> ifeffit-owner(a)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(a)lbl.gov> >> To: ifeffit(a)millenia.cars.aps.anl.gov >> Subject: [Ifeffit] X-ray natural circular dichroism by FEFF? >> Message-ID: <522F48BC.8090402(a)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(a)millenia.cars.aps.anl.gov >> http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit >> >> >> End of Ifeffit Digest, Vol 127, Issue 9 >> *************************************** >

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X-ray natural circular dichroism by FEFF?
by Joshua Kas 11 Sep '13

11 Sep '13

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(a)millenia.cars.aps.anl.gov> wrote: > Send Ifeffit mailing list submissions to > ifeffit(a)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(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)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(a)lbl.gov> > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: [Ifeffit] X-ray natural circular dichroism by FEFF? > Message-ID: <522F48BC.8090402(a)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(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > > End of Ifeffit Digest, Vol 127, Issue 9 > ***************************************

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problem with Demeter on non-unicode machine
by Andrei Shiryaev 07 Sep '13

07 Sep '13

Dear Bruce, I have a problem with running Demeter on non-unicode Win7/64 bit computer. The log file is attached. I am using the latest update and it is better than previous versions since at least something is happening, when I've tried previous Demeter versions, they just crashed immediately. I am not an expert in programming, but I suspect that similar problem existed in one of the old version of IFEFFIT as was discussed with you in July 2008 in the mail list: =============== A followup to the unicode issue: I use a tool called PerlApp to build stand-alone windows executables of my codes. While researching how it handles temporary directory creation, I came across the following: http://bugs.activestate.com/show_bug.cgi?id=43697 It would seem that the issue Kleper and Shiryaev are seeing is the result of that bug, which has been resolved in recent versions of PerlApp. I was certainly using a version of PerlApp that showed this problem when the previous installer was made. I am now using version 7.2, so things should work fine for non-ascii language speakers. I will communicate with Kleper and Shiryaev off the list to ask them to test the new installer. Regards, B ============== I would appreciate some advice how to handle the problem. Regards, Andrei ---------------------------------------------------------------------- -- Andrei Shiryaev

2 3

Installation problems Ubuntu 12.04
by David Eveborn 06 Sep '13

06 Sep '13

Hi! I am trying to install the demeter package from sources as described by Dave Huges https://gist.github.com/waveform80/3959252. I am doing this on a fresh install of ubuntu 12.04 (as a virtual machine if this could have any effect). Most things turns out as expected but I have encountered a problem. When I invoke the ./Build installdeps one single dependency refuses to install because of failing tests. The output from the terminal is attached in this e-mail. If anyone could lead me in how to handle this I would be very happy (I am not experienced in building from sources). Kind Regads David

3 5

chirality and XMCD with FEFF
by Ross Devol 03 Sep '13

03 Sep '13

Hi All, Does anyone know whether FEFF can be used to determine whether a crystal is chiral? I am trying to do this for monohydrocalcite (MHC) using the XMCD card. Would this be the correct approach? Also, while I have gotten FEFF to run with the XMCD card in the feff.inp file for other crystals, I keep getting the following error: "FOLP for POTENTIAL type 4 is too big. Reduce overlap using FOLP and rerun." I've tried FOLP 4 1, FOLP 4 0.8, FOLP 4 0.5, and even FOLP 4 0.2, but I keep getting the same error. Has anyone else had this problem and resolved it? Thank you! Ross DeVol University of Wisconsin-Madison

1 0

Artemis Bug -- Path Like Object
by mattie.peck＠huskers.unl.edu 30 Aug '13

30 Aug '13

Hey Everyone, I've found another bug in Artemis. When I try to add a path like object to the paths list the program crashes. I've attached the log file and copied the text of it below. I'm using the newest version of Artemis 0.9.18.2 and running Windows XP. Thanks, Mattie Peck LOG FILE TEXT BELOW: Started at 2013-08-30T11:27:21 WinXP/.NetMedia Center Edition Service Pack 3 Service Pack 35126002302561 PATH: C:\GPIB_32\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\WINDOWS\system32\WindowsPowerShell\v1.0;C:\Program Files\QuickTime\QTSystem\;C:\strawberry\perl\bin;C:\strawberry\perl\site\bin;C:\strawberry\c\bin;C:\GPIB_32\;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\System32\Wbem;C:\Program Files\Zone Labs\ZoneAlarm\MailFrontier;C:\Program Files\Microsoft SQL Server\90\Tools\binn\;C:\Program Files\QuickTime\QTSystem\;C:\FullProf_Suite perl version: v5.12.3 @INC: C:/strawberry/perl/site/lib C:/strawberry/perl/vendor/lib C:/strawberry/perl/lib . Can't locate object method "pathfinder_index" via package "Demeter::SSPath" at C:/strawberry/perl/site/lib/Demeter/UI/Artemis/Path.pm line 254.

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Artemis Bug
by mattie.peck＠huskers.unl.edu 29 Aug '13

29 Aug '13

Hello, I've got another bug I think. Like I said I'm using the new version of Artemis to open old .apj files and I've noticed that the path information isn't importing correctly. I have opened several .apj files and this problem happens with all of them. I have attached the .apj file and a pdf with screen shots pointing out the discrepancies. I have the latest version of demeter 0.9.18 and I am running Windows XP. Thanks for the help. Sincerely, Mattie Peck

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