Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)
Hi all, Thanks for the insight so far! To give better information re: the system, I am studying quantum dot monolayers. Yes, these diffractograms are powder diffraction images that have been condensed into 1D diffractograms. This is under the condition of laser photoexcitation, and while some signal is thermal (e.g. typical Debye-Waller type decrease of intensity which can be well characterized), I am just trying to better understand the anomalous effects and get a better picture of how the (400) and (200) reflections, and they're relevant atomic coordinates, are related. I can't imagine it being due to dynamic scattering effects as this is a monolayer and my coherence length of my electrons is great! Thanks again! On Wed, Dec 23, 2020 at 7:12 AM Jon Cooper wrote: > Hello, when you say the (4, 0, 0) intensity goes down, I was wondering > what is actually changing? Likewise for the shift in (2, 0, 0). If every > atom lay in a particular diffraction plane, they would all scatter in phase > and the diffraction from that plane would be nice and strong! The relative > phase of each atom's scattering is dictated by the distance from the plane, > right ;-? Diffractogram sounds like proper physics. Best wishes, Jon. C. > > > Sent from ProtonMail mobile > > > > Original Message ---- > On 22 Dec 2020, 22:26, Kamil Krawczyk < kamil.krawczyk7...@gmail.com> > wrote: > > > Hi all, > > As an experimental physicist slowly becoming more acquainted with > crystallography, I have a bit of clerical issue visualizing this particular > problem in my head: > > For example, the 400 and 200 reflections in a diffractogram are related to > the 100 family of crystallographic planes; I'd imagine, that in real space, > the higher order plane (e.g. the 400) corresponds to atoms 'closer' to the > center of the crystal/unit cell. > > I have an interesting observation where I am seeing the 400 peak intensity > go down (likely due to increased RMS motion), whereas the 200 reflection > does not really change in its intensity. Furthermore, I see a shift in the > 200 peak, implying an expansion (a shift to lower q), but no abnormal > change in the 400 peak position. > > What I am having a really hard time wrapping my head around is how these > two events can be occurring simultaneously; I would naively say that since > the 400 reflection is showing an increased RMS, the 400 peak should likely > shift - not the 200. Does anybody have an easy way to visualize this? I am > trying to look at crystallographic vectors in VESTA on a model system, but > sadly have not been able to see the light just yet. > > Thank you! And sorry for dropping all the parentheses on reflection names, > it saved me some typing :p > > > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 > > This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a > mailing list hosted by www.jiscmail.ac.uk, terms & conditions are > available at https://www.jiscmail.ac.uk/policyandsecurity/ > > To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)
Hi all, As an experimental physicist slowly becoming more acquainted with crystallography, I have a bit of clerical issue visualizing this particular problem in my head: For example, the 400 and 200 reflections in a diffractogram are related to the 100 family of crystallographic planes; I'd imagine, that in real space, the higher order plane (e.g. the 400) corresponds to atoms 'closer' to the center of the crystal/unit cell. I have an interesting observation where I am seeing the 400 peak intensity go down (likely due to increased RMS motion), whereas the 200 reflection does not really change in its intensity. Furthermore, I see a shift in the 200 peak, implying an expansion (a shift to lower q), but no abnormal change in the 400 peak position. What I am having a really hard time wrapping my head around is how these two events can be occurring simultaneously; I would naively say that since the 400 reflection is showing an increased RMS, the 400 peak should likely shift - not the 200. Does anybody have an easy way to visualize this? I am trying to look at crystallographic vectors in VESTA on a model system, but sadly have not been able to see the light just yet. Thank you! And sorry for dropping all the parentheses on reflection names, it saved me some typing :p To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
Re: [ccp4bb] Rietveld refinement of polycrystalline electron diffraction data
Hi Dimitris, First, thank you kindly for your wonderful reply - there is a lot of great information to parse through! I will have a look through GSAS and the provided mailing list as well. To quickly add context, here are two images refined to my static structure (compared with experimental data): FM3m starting lattice - https://imgur.com/a/l1HJjLD R3m starting lattice - https://imgur.com/a/805dbOw It seems to me that the FM3m cubic lattice matches peak positions well (fewer reflections overall), but not so much the intensities. However, I think this can likely be refined more. The R3m refinement matches the diffraction well apart from the anomalous peak seen at a 2theta of ~0.85 (this is also the case with FM3m). This peak is not present in the 'excited' structure, which is peculiar, and seems to imply a change in symmetry. The key observable we see crystallographically is a deviation in an expected Debye-Waller-like behaviour, with anomalous peak shifts and intensity changes in reflections related to the (100) plane (e.g. the (200)/(400) reflections). I am thinking there is likely a change of symmetry occurring and hoping to eek it out using refinement. Best, Kamil To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
[ccp4bb] Rietveld refinement of polycrystalline electron diffraction data
Hello! First, apologies if the scope of the question is beyond that of the listserv - I was recommended this discussion page through a colleague. I am incredibly new to refinement, and have been trying to employ the use of Rietveld refinement to better determine the crystal structure of my lead sulfide (PbS) quantum dots. Data was acquired as images on a home-built tabletop time-resolved electron diffraction setup, and converted to diffractogram through a combination of center finding and background subtraction. However, since these are small (~ 5 nm), and we are certainly sampling the ensemble average (as our focused beam is about 120 um in diameter), our pattern is that of a polycrystalline sample. From what I've encountered in my research, Rietveld is best suited for this case. I have taken an initial structure as inferred from literature/the bulk and refined that (relatively successfully to a Rwp value of ~2 - 6%). I do have a few questions regarding this process as I believe I am not being as rigorous as possible: - is there a 'best practices' order of refinement operations? e.g. refine the lattice parameters first, then peak profiles, etc. - there is a single peak that is not matching (likely due to a slight deviation in atomic positions from the expected simple cubic structure) - is refinement capable of moving individual atoms or clusters of atoms to better match a small, unaccounted for reflection? For what it's worth, I have been using Reflex in Materials Studio; if there is a more appropriate software for this application, I would be happy to hear! If any additional clarification is need, I'll fill it in! Best, Kamil To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
