June 2017 - Ifeffit - millenia.cars.aps.anl.gov

Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 6
by Clark, Adam 09 Jun '17

09 Jun '17

Dear Robert Thanks, following the linked discussions I am also now able to repeat the problem though first running a feff calculation on the Rh2O3 structure and second on the Rh structure. Having now downloaded the pre release version this does indeed fix this problem. Adam ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: 09 June 2017 14:16:20 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 172, Issue 6 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: Ifeffit Digest, Vol 172, Issue 4 (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Fri, 9 Jun 2017 06:16:15 -0700 From: Robert Gordon <ragordon(a)alumni.sfu.ca> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 4 Message-ID: <CA+FiM0EcbUaki2K2Zpfb0cFuUHN=tEdLoiun=pMJzQiVMGw-Yg(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Adam, I think the problem you are seeing is related to one observed back in April. The Rh2O3 crystal you also have in your project has trigonal symmetry, and trigonal symmetry in 0.9.25 tends to override all others. This was discussed in this thread: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009083.html Bruce made a pre-release of 0.9.26 available at the time that fixed this problem: http://millenia.cars.aps.anl.gov/pipermail/ifeffit/2017-April/009084.html The pre_2 release of 0.9.26 is also available on the main Demeter page: https://bruceravel.github.io/demeter/ -R. On Fri, Jun 9, 2017 at 5:54 AM, Clark, Adam <adam.clark.14(a)ucl.ac.uk> wrote: > Dear Robert > > > Attached I have given the different feff.inp files generated from using > Artemis and from WebAtoms (named accordingly) along with images showing the > input screens using default parameters. > > > The difference comes in the atoms list generated. Using artemis two short > atoms are produced at 1.91 A which are not present when I use WebAtoms. > Interestingly I have now discovered this does not happen with every artemis > project. I have attached a project where I am getting the erroneous > feff.inp file generation. To replicate the error it is possible to add > another feff calculation into this artemis project with the attached cif. > > > The attached project is an example where this error occurs but I have not > been able thus far to make a new project that repeats this error. > > > Adam > ------------------------------ > *From:* Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of > ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request@millenia. > cars.aps.anl.gov> > *Sent:* 08 June 2017 23:59:09 > *To:* ifeffit(a)millenia.cars.aps.anl.gov > *Subject:* Ifeffit Digest, Vol 172, Issue 4 > > 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: Error using Atoms (Robert Gordon) > 2. Re: question about sigma2 and atomic distance (Robert Gordon) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Thu, 8 Jun 2017 15:33:55 -0700 > From: Robert Gordon <ragordon(a)alumni.sfu.ca> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Error using Atoms > Message-ID: > <CA+FiM0FCdZ5NdupthJLzWrynk2xbXFYE81s5hPVHQrWedqPZow(a)mail.gmail. > com> > Content-Type: text/plain; charset="utf-8" > > Hi Adam, > > I opened the cif file you provided and Artemis/Atoms immediately gave the > atoms.inp file attached. > Running Atoms gave the feff.inp....I don't see a problem. > > Could you provide more detail on how you achieved this erroneous result? > i.e. step by step... > e.g. I opened Artemis v0.9.25 > I clicked 'add' under Feff calculations > I selected Rh.cif and clicked open > et voila! Much humble praise to Bruce... > > -R. > > > > On Thu, Jun 8, 2017 at 5:50 AM, Clark, Adam <adam.clark.14(a)ucl.ac.uk> > wrote: > > > Dear Mailing List > > > > > > I have encountered an issue when using the version of Atoms within > > Artemis for the calculation of the scattering paths on metallic FCC > > systems. Attached are both the cif file and the generated feff.inp file > > from using Atoms from within Artemis. Here the problem that occurs is the > > generation of two short atoms at distances of 1.91 ? before the first > shell > > atoms at distances of 2.70 ? for metallic Rh. > > > > ATOMS * this list contains 69 atoms > > * x y z ipot tag distance > > 0.00000 0.00000 0.00000 0 Rh1 0.00000 > > 1.65411 0.95500 0.00000 1 Rh1.1 1.91000 > > -1.65411 -0.95500 0.00000 1 Rh1.1 1.91000 > > -1.65411 0.95500 1.91000 1 Rh1.2 2.70115 > > 0.00000 1.91000 1.91000 1 Rh1.2 2.70115 > > 1.65411 -0.95500 1.91000 1 Rh1.2 2.70115 > > 0.00000 -1.91000 1.91000 1 Rh1.2 2.70115 > > -1.65411 0.95500 -1.91000 1 Rh1.2 2.70115 > > 0.00000 1.91000 -1.91000 1 Rh1.2 2.70115 > > 1.65411 -0.95500 -1.91000 1 Rh1.2 2.70115 > > 0.00000 -1.91000 -1.91000 1 Rh1.2 2.70115 > > > > > > Using the same input CIF file within WebAtoms does not produce these > short > > distances. > > > > > > Adam Clark > > > > > > PhD Student > > > > > > > > Industrial Doctorate Centre in Molecular Modelling and Materials Science, > > > > Department of Chemistry, > > > > University College London > > > > > > _______________________________________________ > > Ifeffit mailing list > > Ifeffit(a)millenia.cars.aps.anl.gov > > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > > > > >

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Re: [Ifeffit] Ifeffit Digest, Vol 172, Issue 4
by Clark, Adam 09 Jun '17

09 Jun '17

Dear Robert Attached I have given the different feff.inp files generated from using Artemis and from WebAtoms (named accordingly) along with images showing the input screens using default parameters. The difference comes in the atoms list generated. Using artemis two short atoms are produced at 1.91 A which are not present when I use WebAtoms. Interestingly I have now discovered this does not happen with every artemis project. I have attached a project where I am getting the erroneous feff.inp file generation. To replicate the error it is possible to add another feff calculation into this artemis project with the attached cif. The attached project is an example where this error occurs but I have not been able thus far to make a new project that repeats this error. Adam ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: 08 June 2017 23:59:09 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 172, Issue 4 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: Error using Atoms (Robert Gordon) 2. Re: question about sigma2 and atomic distance (Robert Gordon) ---------------------------------------------------------------------- Message: 1 Date: Thu, 8 Jun 2017 15:33:55 -0700 From: Robert Gordon <ragordon(a)alumni.sfu.ca> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Error using Atoms Message-ID: <CA+FiM0FCdZ5NdupthJLzWrynk2xbXFYE81s5hPVHQrWedqPZow(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Adam, I opened the cif file you provided and Artemis/Atoms immediately gave the atoms.inp file attached. Running Atoms gave the feff.inp....I don't see a problem. Could you provide more detail on how you achieved this erroneous result? i.e. step by step... e.g. I opened Artemis v0.9.25 I clicked 'add' under Feff calculations I selected Rh.cif and clicked open et voila! Much humble praise to Bruce... -R. On Thu, Jun 8, 2017 at 5:50 AM, Clark, Adam <adam.clark.14(a)ucl.ac.uk> wrote: > Dear Mailing List > > > I have encountered an issue when using the version of Atoms within > Artemis for the calculation of the scattering paths on metallic FCC > systems. Attached are both the cif file and the generated feff.inp file > from using Atoms from within Artemis. Here the problem that occurs is the > generation of two short atoms at distances of 1.91 ? before the first shell > atoms at distances of 2.70 ? for metallic Rh. > > ATOMS * this list contains 69 atoms > * x y z ipot tag distance > 0.00000 0.00000 0.00000 0 Rh1 0.00000 > 1.65411 0.95500 0.00000 1 Rh1.1 1.91000 > -1.65411 -0.95500 0.00000 1 Rh1.1 1.91000 > -1.65411 0.95500 1.91000 1 Rh1.2 2.70115 > 0.00000 1.91000 1.91000 1 Rh1.2 2.70115 > 1.65411 -0.95500 1.91000 1 Rh1.2 2.70115 > 0.00000 -1.91000 1.91000 1 Rh1.2 2.70115 > -1.65411 0.95500 -1.91000 1 Rh1.2 2.70115 > 0.00000 1.91000 -1.91000 1 Rh1.2 2.70115 > 1.65411 -0.95500 -1.91000 1 Rh1.2 2.70115 > 0.00000 -1.91000 -1.91000 1 Rh1.2 2.70115 > > > Using the same input CIF file within WebAtoms does not produce these short > distances. > > > Adam Clark > > > PhD Student > > > > Industrial Doctorate Centre in Molecular Modelling and Materials Science, > > Department of Chemistry, > > University College London > > > _______________________________________________ > Ifeffit mailing list > Ifeffit(a)millenia.cars.aps.anl.gov > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > Unsubscribe: http://millenia.cars.aps.anl.gov/mailman/options/ifeffit > >

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q2xafs2017 in August
by fred.mosselmans＠diamond.ac.uk 08 Jun '17

08 Jun '17

Hi For those of you that are not aware, Q2XAFS2017 (the International Workshop on Improving Data Quality in XAFS Spectroscopy) is taking place at Diamond Light Source near Oxford, which is where the spires dream, on 14/15 August this summer. See http://www.q2xafs2017.com/ for details / registration Although the abstract deadline is currently listed as 5th June, it will be shortly extended to early July. We hope to see you in England Regards Fred J.F.W. Mosselmans Principal Beamline Scientist I18 Diamond Light Source Ltd Diamond House Harwell Campus Didcot OX11 0DE P + 44 1235 778568 M + 44 7785510211 E fred.mosselmans(a)diamond.ac.uk orcid.org/0000-0001-6473-2743 [cid:image002.png@01D27563.28EDA240] -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom

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Error using Atoms
by Clark, Adam 08 Jun '17

08 Jun '17

Dear Mailing List I have encountered an issue when using the version of Atoms within Artemis for the calculation of the scattering paths on metallic FCC systems. Attached are both the cif file and the generated feff.inp file from using Atoms from within Artemis. Here the problem that occurs is the generation of two short atoms at distances of 1.91 Å before the first shell atoms at distances of 2.70 Å for metallic Rh. ATOMS * this list contains 69 atoms * x y z ipot tag distance 0.00000 0.00000 0.00000 0 Rh1 0.00000 1.65411 0.95500 0.00000 1 Rh1.1 1.91000 -1.65411 -0.95500 0.00000 1 Rh1.1 1.91000 -1.65411 0.95500 1.91000 1 Rh1.2 2.70115 0.00000 1.91000 1.91000 1 Rh1.2 2.70115 1.65411 -0.95500 1.91000 1 Rh1.2 2.70115 0.00000 -1.91000 1.91000 1 Rh1.2 2.70115 -1.65411 0.95500 -1.91000 1 Rh1.2 2.70115 0.00000 1.91000 -1.91000 1 Rh1.2 2.70115 1.65411 -0.95500 -1.91000 1 Rh1.2 2.70115 0.00000 -1.91000 -1.91000 1 Rh1.2 2.70115 Using the same input CIF file within WebAtoms does not produce these short distances. Adam Clark PhD Student Industrial Doctorate Centre in Molecular Modelling and Materials Science, Department of Chemistry, University College London

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artemis results not reproducible
by Loges, Anselm G 06 Jun '17

06 Jun '17

Dear fellow EXAFSeteers, I have a somewhat bizarre problem with Artemis fits. I am using Demeter 0.9.25 64bit on a Windows7 machine. The Situation: I am trying to fit the first shell complexing ligands to aqueous metal complexes. I have sets of experiments at different temperatures but otherwise identical conditions and concentrations. When I fit all experiments separately, parameters such as coordination number and metal-ligand distance show systematic variation with temperature (as they should). Therefore, I would like to try fitting all these experiments together and define these parameters as functions of temperature, which would reduce the total number of free parameters relative to the experimental points and should also bring the uncertainties down a bit. To this end, I first made an Artemis project that contains several of the data sets (at different temperatures). Then I made individual parameters for each data set that are exactly as they are in the individual fits (parameter names are different, though) and duplicated the fourier transform parameters of the individual fits. Now each data set has its own set of parameters. No parameters are shared between data sets and there are no connections between data sets via "def" functions in the GDS or anything. The Problem: When start the fit, I get different results from the individual fits. Still mostly within the calculated error values (which are quite large at the moment), so not "significantly different" in the statistical sense of the words but still very different numbers. Whats more, if I add another data set with corresponding parameters (again no connection to the other data sets or parameters), the results for the parameters of the other data sets change again. Am I right in assuming that this should not be the case or is there a connection which I am missing? Might this be a bug? Some fits react a bit sensitive to the choice of k- and R-space windows (but these were identical in individual and simultaneous fits). My fits are pushing the number of independent parameters a bit, according to the log-files (which is why I want to do the simultaneous fits with T-dependent parameters). Might this cause instability in the fit routine. In the simultaneous fits, the number of highly correlated parameters (>0.95) skyrockets (is ok in individual fits), which may be related to the next point. I suspect it may also have to do with the way Artemis decides that the fit is "done". If this is evaluated globally for all parameters somehow, then the observed behavior would not be surprising. But if it is evaluated on a per-parameter or per-data set basis, then it should not be like this. Finally: Is my approach reasonable at all or is that a bad idea? Does someone else use this method? I have not seen it published but then again I am new to this and many publications are a bit reserved on the topic of fitting strategy. Thanks a lot and sorry for the long read, Anselm

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