Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

2020-12-27 Thread Bernhard Rupp 
In addition to the Debye-Waller correction, you have additional attenuation 
from the Lorenz and Geometry factor (specific for your powder diffraction 
geometry) that convolutes with the DB apodization.

 

Meaning: the 400 will be more attenuated relative to 200 if you correct only 
for DBW.

 

A peak shift is not explained this way, because larger B and LPG only affect 
intensity. A cell change should affect both reflections similarly (Bragg). The 
whole intensity thing falls apart if you have in addition preferred orientation 
effects, but I do not know enough about your sort of experiment to say whether 
this is possible. Can monolayers warp or something like anisotropically expand?

 

Best, BR

 

From: CCP4 bulletin board  On Behalf Of Kamil Krawczyk
Sent: Thursday, December 24, 2020 15:22
To: CCP4BB@JISCMAIL.AC.UK
Subject: 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 mailto:jon.b.coo...@protonmail.com> > 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



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Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

2020-12-25 Thread Dom Bellini 

Hi Kamil, 

Ok this gives a better picture of the experiment. Although electron density 
contribution to diffraction is a bit more complicated than what I said in my 
previous email, in essence though the diffracting angles of 200 and 400 are 
indeed related as you said, with sin(theta) equal to lambda/2d and 
lambda/2(d/2), respectively. Therefore a shift of the 200, which implies 
distortion of the original unit cell (or change in wavelength), should also 
mean a shift of 400. I cannot see why that would not be the case; even the 
presence of anomalous signal as you suggested should cause changes to intensity 
and phase of the reflection but not to the scattering angle? At least not to 
only one of either 200 or 400? Perhaps other may have an explanation for ... 
once their Christmas lunch is over!

BW,

D

> On 24 Dec 2020, at 23:23, Kamil Krawczyk  wrote:
> 
> 
> 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/
>> 
> 
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Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

2020-12-24 Thread Kamil Krawczyk 
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/
>
>



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Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

2020-12-23 Thread Jon Cooper 
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 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/



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Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

2020-12-22 Thread Dom Bellini 
> 
> 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.
> 

If it can help you to work out an explanation for what you are observing, the 
higher order reflection 400 does not correspond to atoms closer to the centre 
of the unit cell but, compared to reflection 200, it also contains diffraction 
contributions from atoms that are placed exactly half way between two 
consecutive 200 planes. 

BW,

D


> 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 
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> 
> 
> 
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Re: [ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

2020-12-22 Thread Bernhard Rupp 
A situation like you are describing can happen in small molecule and power 
diffraction. If you explain what you are actually doing, it might be possible 
to speculate...

Best, BR 

-Original Message-
From: CCP4 bulletin board  On Behalf Of Kamil Krawczyk
Sent: Tuesday, December 22, 2020 14:27
To: CCP4BB@JISCMAIL.AC.UK
Subject: [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



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[ccp4bb] Relationship of crystallographic planes and reflections, e.g. (200) and (400)

2020-12-22 Thread Kamil Krawczyk 
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

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