Re: [sdpd] Re: Are restraints as good as observations ?
Leonid, I suggest you to try K4P2O7 - synchrotron data... If you send me the data I may try. OK. K4P2O7 at room temperature is a good example for your horror museum of bad things done in the SDPD world and which could have been so much better if DDM was used. This case belongs to the acentric class of problems. Acentricity leads to a 2 times more unfavourable (atomic coordinates)/data ratio than for centric compounds. This is also the case for beta-Ba3AlF9 for which I can send the original 1993 data, if you wish, and you may see if Al-F distances are convincing without restraints using DDM (I obtained crazy Al-F distances in the 1.65-1.97 A range, instead of 1.81+-0.04 A for usually regular AlF6 octahedra). BTW, try to solve the structure before the Rietveld fif. Best, Armel ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
Re: [sdpd] Re: Are restraints as good as observations ?
Leonid, I suggest you to try K4P2O7 - synchrotron data, space group P61 - for which I had to put distance restraints on the three P2O7 independent groups - Powder Diffraction, 28, 2-12, 2013 Done without restraints: http://sites.google.com/site/ddmsuite/tutorials/K4P2O7-DDM.cif Only Biso of chemically equivalent O-atoms are constrained, while this is not absolutely necessary. The DDM plot: http://sites.google.com/site/ddmsuite/tutorials/K4P2O7-plot.png Characteristic distances: P1-O1 1.530(30) P2-O2 1.548(32) P3-O7 1.536(29) P1-O3 1.499(26) P2-O4 1.502(23) P3-O9 1.481(31) P1-O5 1.580(28) P2-O6 1.521(36) P3-O11 1.542(24) P1-O13 1.614(30) P2-O14 1.576(32) P3-O14 1.719(30) P4-O8 1.552(37) P5-O15 1.518(24) P6-O18 1.551(31) P4-O10 1.482(22) P5-O16 1.553(37) P6-O19 1.536(23) P4-O12 1.540(34) P5-O17 1.498(32) P6-O20 1.486(37) P4-O13 1.689(32) P5-O21 1.600(28) P6-O21 1.674(29) All deviations from expected values (1.514 and 1.634) are within 3 e.s.u.s that are around 0.03 A in average. Further improvements seem possible, but it will require more time and efforts. So, one more example of underestimated information capacity of powder data and overestimated necessity of restraints. *** Leonid A. Solovyov Institute of Chemistry and Chemical Technology 660049, K. Marx 42, Krasnoyarsk, Russia http://sites.google.com/site/solovyovleonid *** From: xtal x...@noos.fr To: s...@yahoogroups.com; rietveld_l@ill.fr rietveld_l@ill.fr Sent: Thursday, August 1, 2013 3:10 PM Subject: Re: [sdpd] Re: Are restraints as good as observations ? Leonid, I suggest you to try K4P2O7 - synchrotron data... If you send me the data I may try. OK. K4P2O7 at room temperature is a good example for your horror museum of bad things done in the SDPD world and which could have been so much better if DDM was used. This case belongs to the acentric class of problems. Acentricity leads to a 2 times more unfavourable (atomic coordinates)/data ratio than for centric compounds. This is also the case for beta-Ba3AlF9 for which I can send the original 1993 data, if you wish, and you may see if Al-F distances are convincing without restraints using DDM (I obtained crazy Al-F distances in the 1.65-1.97 A range, instead of 1.81+-0.04 A for usually regular AlF6 octahedra). BTW, try to solve the structure before the Rietveld fif. Best, Armel++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
Re: [sdpd] Re: Are restraints as good as observations ?
All deviations from expected values (1.514 and 1.634) are within 3 e.s.u.s that are around 0.03 A in average. Further improvements seem possible, but it will require more time and efforts. So, one more example of underestimated information capacity of powder data and overestimated necessity of restraints. What information capacity ? The fact is that imposing the expected values you obtain a similar fit. This tells you that you cannot discuss your unrestrained information, because it is unreliable. Information is something you may discuss reliably. The only possible discussion about P3-O14 = 1.72(3)A is to say that it is very probably strongly overestimated. Such are powder results for complex cases. Sure, the restrained distances cannot be discussed as well. At least they are not completely extravagant. Best Armel ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
Re: [sdpd] Re: Are restraints as good as observations ?
What information capacity ? The fact is that imposing the expected values you obtain a similar fit. This tells you that you cannot discuss your unrestrained information, because it is unreliable. Information is something you may discuss reliably. The only possible discussion about P3-O14 = 1.72(3)A is to say that it is very probably strongly overestimated. After THIS unrestrained refinement one CAN discuss RELIABLY ALL interatomic distances including P-O, K-O, K-P, K-K and P-P, as well as angles, orientations etc., WITHIN THEIR UNCERTAINTIES that are also estimated RELIABLY according to the EXPERIMENTALLY DETERMINED deviations of the unrestrained P-O distances. After the restrained refinement NOTHING can be discussed RELIABLY since neither the values nor their uncertainties are determined EXPERIMENTALLY. After the unrestrained refinement one can state RELIABLY that the structure is DETERMINED with definite precision and, thus, discuss its features, compare it with other experimentally determined structures within their uncertainties, make more or less definite conclusions etc. After the restrained refinement one can only state that a hypothetical structure model is proposed and NOTHING can be concluded or discussed RELIABLY. Don't you see the difference??!! Determination = reliable experimental evaluation + reliable estimation of uncertainties. Now I probably understand your colleagues. *** Leonid A. Solovyov Institute of Chemistry and Chemical Technology 660049, K. Marx 42, Krasnoyarsk, Russia http://sites.google.com/site/solovyovleonid *** From: Armel Le Bail x...@noos.fr To: s...@yahoogroups.com Cc: rietveld_l@ill.fr Sent: Friday, August 2, 2013 12:40 AM Subject: Re: [sdpd] Re: Are restraints as good as observations ? All deviations from expected values (1.514 and 1.634) are within 3 e.s.u.s that are around 0.03 A in average. Further improvements seem possible, but it will require more time and efforts. So, one more example of underestimated information capacity of powder data and overestimated necessity of restraints. What information capacity ? The fact is that imposing the expected values you obtain a similar fit. This tells you that you cannot discuss your unrestrained information, because it is unreliable. Information is something you may discuss reliably. The only possible discussion about P3-O14 = 1.72(3)A is to say that it is very probably strongly overestimated. Such are powder results for complex cases. Sure, the restrained distances cannot be discussed as well. At least they are not completely extravagant. Best Armel ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
RE: [sdpd] Re: Are restraints as good as observations ?
At the end it is all wrong as we don’t refine individual electrons but restrained groups that are called “atoms” which are extrapolated with some average function calculated for free, unbounded atom. Peter Zavalij From: rietveld_l-requ...@ill.fr [mailto:rietveld_l-requ...@ill.fr] On Behalf Of Leonid Solovyov Sent: Thursday, August 01, 2013 7:33 PM To: s...@yahoogroups.com Cc: rietveld_l@ill.fr Subject: Re: [sdpd] Re: Are restraints as good as observations ? What information capacity ? The fact is that imposing the expected values you obtain a similar fit. This tells you that you cannot discuss your unrestrained information, because it is unreliable. Information is something you may discuss reliably. The only possible discussion about P3-O14 = 1.72(3)A is to say that it is very probably strongly overestimated. After THIS unrestrained refinement one CAN discuss RELIABLY ALL interatomic distances including P-O, K-O, K-P, K-K and P-P, as well as angles, orientations etc., WITHIN THEIR UNCERTAINTIES that are also estimated RELIABLY according to the EXPERIMENTALLY DETERMINED deviations of the unrestrained P-O distances. After the restrained refinement NOTHING can be discussed RELIABLY since neither the values nor their uncertainties are determined EXPERIMENTALLY. After the unrestrained refinement one can state RELIABLY that the structure is DETERMINED with definite precision and, thus, discuss its features, compare it with other experimentally determined structures within their uncertainties, make more or less definite conclusions etc. After the restrained refinement one can only state that a hypothetical structure model is proposed and NOTHING can be concluded or discussed RELIABLY. Don't you see the difference??!! Determination = reliable experimental evaluation + reliable estimation of uncertainties. Now I probably understand your colleagues. *** Leonid A. Solovyov Institute of Chemistry and Chemical Technology 660049, K. Marx 42, Krasnoyarsk, Russia http://sites.google.com/site/solovyovleonid *** From: Armel Le Bail x...@noos.frmailto:x...@noos.fr To: s...@yahoogroups.commailto:s...@yahoogroups.com Cc: rietveld_l@ill.frmailto:rietveld_l@ill.fr Sent: Friday, August 2, 2013 12:40 AM Subject: Re: [sdpd] Re: Are restraints as good as observations ? All deviations from expected values (1.514 and 1.634) are within 3 e.s.u.s that are around 0.03 A in average. Further improvements seem possible, but it will require more time and efforts. So, one more example of underestimated information capacity of powder data and overestimated necessity of restraints. What information capacity ? The fact is that imposing the expected values you obtain a similar fit. This tells you that you cannot discuss your unrestrained information, because it is unreliable. Information is something you may discuss reliably. The only possible discussion about P3-O14 = 1.72(3)A is to say that it is very probably strongly overestimated. Such are powder results for complex cases. Sure, the restrained distances cannot be discussed as well. At least they are not completely extravagant. Best Armel ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
RE: [sdpd] Re: Are restraints as good as observations ?
Hi all, I have been following the tennis match going on here, and I'll point out what Brian Toby said again - use the data you have to fit what you can. When my work strongly focused on this I too used to be stuck on the fact that macromolecular crystallographers can use ultra-low resolution data... until I figured out they're not doing the same thing as people doing large small molecule work. So on the reliability of structures, how reliable is a DFT optimized structure... I know that theoreticians can calculate and optimize almost anything, which does not mean the result has any bearing on reality. Is it a result that was DFTized more reliable than a poorly converging result based on experimental data from a fit? And if you want to discuss the philosophy of restraints/constraints, we were not the ones that invented Tikhonov regularization and Levenberg-Marquardt fitting - sometimes when fitting a Jacobian with a poor quality number it is the only way to approach a stable solution... Alex Y ___ Dr. Alexandre (Alex) F. T. Yokochi Associate Professor of Chemical Engineering Laboratory for innovative Reaction Engineering for Materials and Sustainability (iREMS lab) School of Chemical, Biological and Environmental Engineering Oregon State University Corvallis, OR 97331 - 2702 -Original Message- From: s...@yahoogroups.com [mailto:s...@yahoogroups.com] On Behalf Of Leonid Solovyov Sent: Thursday, August 01, 2013 4:33 PM To: s...@yahoogroups.com Cc: rietveld_l@ill.fr Subject: Re: [sdpd] Re: Are restraints as good as observations ? What information capacity ? The fact is that imposing the expected values you obtain a similar fit. This tells you that you cannot discuss your unrestrained information, because it is unreliable. Information is something you may discuss reliably. The only possible discussion about P3-O14 = 1.72(3)A is to say that it is very probably strongly overestimated. After THIS unrestrained refinement one CAN discuss RELIABLY ALL interatomic distances including P-O, K-O, K-P, K-K and P-P, as well as angles, orientations etc., WITHIN THEIR UNCERTAINTIES that are also estimated RELIABLY according to the EXPERIMENTALLY DETERMINED deviations of the unrestrained P-O distances. After the restrained refinement NOTHING can be discussed RELIABLY since neither the values nor their uncertainties are determined EXPERIMENTALLY. After the unrestrained refinement one can state RELIABLY that the structure is DETERMINED with definite precision and, thus, discuss its features, compare it with other experimentally determined structures within their uncertainties, make more or less definite conclusions etc. After the restrained refinement one can only state that a hypothetical structure model is proposed and NOTHING can be concluded or discussed RELIABLY. Don't you see the difference??!! Determination = reliable experimental evaluation + reliable estimation of uncertainties. Now I probably understand your colleagues. *** Leonid A. Solovyov Institute of Chemistry and Chemical Technology 660049, K. Marx 42, Krasnoyarsk, Russia http://sites.google.com/site/solovyovleonid *** From: Armel Le Bail x...@noos.fr To: s...@yahoogroups.com Cc: rietveld_l@ill.fr Sent: Friday, August 2, 2013 12:40 AM Subject: Re: [sdpd] Re: Are restraints as good as observations ? All deviations from expected values (1.514 and 1.634) are within 3 e.s.u.s that are around 0.03 A in average. Further improvements seem possible, but it will require more time and efforts. So, one more example of underestimated information capacity of powder data and overestimated necessity of restraints. What information capacity ? The fact is that imposing the expected values you obtain a similar fit. This tells you that you cannot discuss your unrestrained information, because it is unreliable. Information is something you may discuss reliably. The only possible discussion about P3-O14 = 1.72(3)A is to say that it is very probably strongly overestimated. Such are powder results for complex cases. Sure, the restrained distances cannot be discussed as well. At least they are not completely extravagant. Best Armel [Non-text portions of this message have been removed] Yahoo! Groups Links * To visit your group on the web, go to: http://groups.yahoo.com/group/sdpd/ * Your email settings: Individual Email | Traditional * To change settings online go to: http://groups.yahoo.com/group/sdpd/join (Yahoo! ID required) * To change settings via email: sdpd-dig...@yahoogroups.com sdpd-fullfeatu...@yahoogroups.com * To unsubscribe from this group, send an email to: sdpd-unsubscr...@yahoogroups.com * Your use of Yahoo! Groups is subject to:
Re: [sdpd] Re: Are restraints as good as observations ?
At the end it is all wrong as we don’t refine individual electrons but restrained groups that are called “atoms” which are extrapolated with some average function calculated for free, unbounded atom. If you mean the scattering curves - they are not restrained, but rigidly constrained and these constraints are definitely and equally specified in all crystallographic programs, which allows comparing the refinement results and making reliable conclusions. In exceptional cases the scattering curves may as well be refined if the data permit. *** Leonid A. Solovyov Institute of Chemistry and Chemical Technology 660049, K. Marx 42, Krasnoyarsk, Russia http://sites.google.com/site/solovyovleonid *** From: Peter Y. Zavalij pzava...@umd.edu To: Leonid Solovyov l_solov...@yahoo.com; s...@yahoogroups.com s...@yahoogroups.com Cc: rietveld_l@ill.fr rietveld_l@ill.fr Sent: Friday, August 2, 2013 6:59 AM Subject: RE: [sdpd] Re: Are restraints as good as observations ? At the end it is all wrong as we don’t refine individual electrons but restrained groups that are called “atoms” which are extrapolated with some average function calculated for free, unbounded atom. Peter Zavalij++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
Re: [sdpd] Re: Are restraints as good as observations ?
At the end it is all wrong as we don’t refine individual electrons... I think we have heard enough when the argument turns to Reductio ad absurdum You might also say that Rietveld refinement by its nature is restrained because we restrain the peaks to positions that are determined by the the assumed average crystal lattice. We could otherwise, and do with PDF analysis, simply Fourier transform the diffraction pattern to obtain the pair correlation pattern, which in the end is the only real-space information available. As Leonid says, in some cases we might even try to determine the electron distribution. But there is a difference when we publish a structure as a Rietveld Refinement, when in fact most of the information comes from restraints and not measured data. Yes if you have a complex structure and relatively poor data, you might want to restrain your model in order to say something about it. But the most you can then say is that the restrained model is consistent with the data. As Leonid says, when you restrain parameters in your model that would otherwise correlate with refined parameters (that is why you restrain them), the calculated standard deviations of the remaining refined parameters are underestimated (not improved). FYI: The greater restraints to parameters ratio the better. AT the end restraints are observations. S it is not about restraints... That was the statement that shocked me :-) and which started this unfortunate thread. As for x-ray powder refinements of heavy metal oxides, there are over 60 entries in ICSD for Mo-oxides. These oxides are often non-stoichiometric, probably due to mixed valence, have various phases or even mixed phases and even non-commensurate phases (actually block structures of different stoichiometry). Such materials are difficult to study with x-rays anyway, because of the heavy atoms as well as all kinds of x-ray powder experimental problems, including of course the powder averaging itself. When Armel praises such x-ray powder refinements as the most complex yet attempted, I suspect he is being a little sarcastic :-) Much as I admire Rietveld refinement, there are some problems for which it is simply not suitable. Hugo Rietveld himself thought that it would never be applied for x-rays because of the systematic errors, but of course he was wrong :-) People are happy now to apply black box Rietveld programs, refining all kinds of sophisticated sample-experiment corrections to improve their R-factor, and then having to add constraints to ensure that the resulting structure looks good enough to publish. OK, but when they say that the more restraints the better, some of us don't agree. Let's leave it at that. Alan __ Dr Alan Hewat, NeutronOptics, Grenoble, FRANCE alan.he...@neutronoptics.com +33.476.98.41.68 http://www.NeutronOptics.com/hewat __ ++ Please do NOT attach files to the whole list alan.he...@neutronoptics.com Send commands to lists...@ill.fr eg: HELP as the subject with no body text The Rietveld_L list archive is on http://www.mail-archive.com/rietveld_l@ill.fr/ ++
