Re: [ccp4bb] Rietveld refinement of polycrystalline electron diffraction data

2020-11-12 Thread Kamil Krawczyk
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



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Re: [ccp4bb] Rietveld refinement of polycrystalline electron diffraction data

2020-11-12 Thread Tim Gruene
Dear Paulina,

you can find plenty  of names of experts on electron powder
diffraction at this announcement of the ePDF workshop,
https://www.uni-ulm.de/einrichtungen/hrem/epdf/epdf/, organised by
Tatiana Gorelik.

They can probably answer your question

Best regards,
Tim 

On Thu, 12 Nov 2020 08:40:32 +0100
Paulina Dominiak  wrote:

> Dear Kamil and Dimitris,
> 
> I wonder what kind of scattering factors are mentioned below programs 
> using for Rietfveld refinement? Are these from IT for electron
> scattering?
> 
> Best,
> 
> Paulina
> 
> 
> W dniu 12.11.2020 o 07:35, Dimitris Triandafillidis pisze:
> > Dear Kamil,
> >
> > Since you have an initial model that is presumably close to what
> > you expect to find in your sample, then Rietveld refinement is the
> > right choice. In cases where no initial model is available, other
> > types of refinement are suitable, such as Pawley or Le Bail, which
> > refine lattice and peak shape parameters only.
> >
> > Regarding the order in which parameters are introduced to a fit, a 
> > good starting point would be:
> > - lattice parameters and zero shift
> > - peak shape parameters and scale factor
> > - background terms
> > - atomic positions
> > Depending on the quality of your data and the nature of your
> > sample, more parameters could be refined (i.e. atomic displacement
> > parameters, preferred orientation, absorption etc.).
> >
> > My suggestion would be to get a better understanding of the effect
> > of each parameter to the fit, in order to troubleshoot your
> > refinement more effectively. For example, peak positions depend on
> > lattice parameters (and space group setting), therefore refining
> > e.g. the scale factor would not help much if expected peak
> > positions are in the wrong place. The following article might be
> > helpful to you. McCusker, L.B., Von Dreele, R.B., Cox, D.E., Louër,
> > D., Scardi, P., 1999. Rietveld refinement guidelines. Journal of
> > Applied Crystallography 32, 36–50.
> > https://dx.doi.org/10.1107/S0021889898009856
> >
> > As for the single peak not being explained by the fit, it could be
> > due to deviations in lattice parameters, but in that case more than
> > one peak would not match. If every other peak fits nicely and only
> > one does not, I would think that it is due to coexistance of a
> > second, trace, crystalline phase in the sample. In most refinement
> > software you have the option of excluding a peak from refinement.
> > Refining atomic positions would not help, as these change the
> > relative peak intensities, not peak positions. However, if you
> > could share a few images of the fit, it would really help to better
> > understand what's going on.
> >
> > Finally, with regards to software, you could also try GSAS 
> > . It is one of the 
> > most widely used software for powder diffraction and it is free.
> > There is also a mailing list 
> > , consisting 
> > mainly of powder diffractionists, and a handful collection of 
> > tutorials 
> > .
> >
> > Best wishes,
> > Dimitris
> >
> >
> > On Thu, Nov 12, 2020 at 12:18 AM Kamil Krawczyk 
> >  > > wrote:
> >
> > 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 

Re: [ccp4bb] Rietveld refinement of polycrystalline electron diffraction data

2020-11-11 Thread Paulina Dominiak

Dear Kamil and Dimitris,

I wonder what kind of scattering factors are mentioned below programs 
using for Rietfveld refinement? Are these from IT for electron scattering?


Best,

Paulina


W dniu 12.11.2020 o 07:35, Dimitris Triandafillidis pisze:

Dear Kamil,

Since you have an initial model that is presumably close to what you 
expect to find in your sample, then Rietveld refinement is the right 
choice. In cases where no initial model is available, other types of 
refinement are suitable, such as Pawley or Le Bail, which refine 
lattice and peak shape parameters only.


Regarding the order in which parameters are introduced to a fit, a 
good starting point would be:

- lattice parameters and zero shift
- peak shape parameters and scale factor
- background terms
- atomic positions
Depending on the quality of your data and the nature of your sample, 
more parameters could be refined (i.e. atomic displacement parameters, 
preferred orientation, absorption etc.).


My suggestion would be to get a better understanding of the effect of 
each parameter to the fit, in order to troubleshoot your refinement 
more effectively. For example, peak positions depend on lattice 
parameters (and space group setting), therefore refining e.g. the 
scale factor would not help much if expected peak positions are in the 
wrong place. The following article might be helpful to you.
McCusker, L.B., Von Dreele, R.B., Cox, D.E., Louër, D., Scardi, P., 
1999. Rietveld refinement guidelines. Journal of Applied 
Crystallography 32, 36–50. https://dx.doi.org/10.1107/S0021889898009856


As for the single peak not being explained by the fit, it could be due 
to deviations in lattice parameters, but in that case more than one 
peak would not match. If every other peak fits nicely and only one 
does not, I would think that it is due to coexistance of a second, 
trace, crystalline phase in the sample. In most refinement software 
you have the option of excluding a peak from refinement. Refining 
atomic positions would not help, as these change the relative peak 
intensities, not peak positions. However, if you could share a few 
images of the fit, it would really help to better understand what's 
going on.


Finally, with regards to software, you could also try GSAS 
. It is one of the 
most widely used software for powder diffraction and it is free. There 
is also a mailing list 
, consisting 
mainly of powder diffractionists, and a handful collection of 
tutorials 
.


Best wishes,
Dimitris


On Thu, Nov 12, 2020 at 12:18 AM Kamil Krawczyk 
mailto:kamil.krawczyk7...@gmail.com>> 
wrote:


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



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Re: [ccp4bb] Rietveld refinement of polycrystalline electron diffraction data

2020-11-11 Thread Dimitris Triandafillidis
Dear Kamil,

Since you have an initial model that is presumably close to what you expect
to find in your sample, then Rietveld refinement is the right choice. In
cases where no initial model is available, other types of refinement are
suitable, such as Pawley or Le Bail, which refine lattice and peak shape
parameters only.

Regarding the order in which parameters are introduced to a fit, a good
starting point would be:
- lattice parameters and zero shift
- peak shape parameters and scale factor
- background terms
- atomic positions
Depending on the quality of your data and the nature of your sample, more
parameters could be refined (i.e. atomic displacement parameters, preferred
orientation, absorption etc.).

My suggestion would be to get a better understanding of the effect of each
parameter to the fit, in order to troubleshoot your refinement more
effectively. For example, peak positions depend on lattice parameters (and
space group setting), therefore refining e.g. the scale factor would not
help much if expected peak positions are in the wrong place. The following
article might be helpful to you.
McCusker, L.B., Von Dreele, R.B., Cox, D.E., Louër, D., Scardi, P., 1999.
Rietveld refinement guidelines. Journal of Applied Crystallography 32,
36–50. https://dx.doi.org/10.1107/S0021889898009856

As for the single peak not being explained by the fit, it could be due to
deviations in lattice parameters, but in that case more than one peak would
not match. If every other peak fits nicely and only one does not, I would
think that it is due to coexistance of a second, trace, crystalline phase
in the sample. In most refinement software you have the option of excluding
a peak from refinement. Refining atomic positions would not help, as these
change the relative peak intensities, not peak positions. However, if you
could share a few images of the fit, it would really help to better
understand what's going on.

Finally, with regards to software, you could also try GSAS
. It is one of the most
widely used software for powder diffraction and it is free. There is
also a mailing
list , consisting
mainly of powder diffractionists, and a handful collection of tutorials
.

Best wishes,
Dimitris


On Thu, Nov 12, 2020 at 12:18 AM Kamil Krawczyk <
kamil.krawczyk7...@gmail.com> wrote:

> 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
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>



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[ccp4bb] Rietveld refinement of polycrystalline electron diffraction data

2020-11-11 Thread Kamil Krawczyk
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



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