xrayutilities-users — User mailinglist for xrayutilities

[Xrayutilities-users] RSM from tiff-files

[Pussi K. (LUKE) <kat...@lu...>]

Hi,

Has anyone experience with creating reciprocal space maps from tiff files? I have old data from Spring8 which includes tiff and txt files. I wonder if anyone has script for extracting RSM from these?

Katariina

Re: [Xrayutilities-users] thin film roughness

[Dominik K. <dom...@gm...>]

Dear Rajesh,

thanks for sharing the discussion with the mailing list!
Let me just point out that the resolution is likely not a very good fitting
parameter. I prefer to manually adjust it since the numerical fit can
quickly arrive at unrealistic values.

kind regards
Dominik

On Mon, Sep 8, 2025 at 10:29 PM Dutta,Rajesh <rd...@dr...> wrote:

> Hi Domink,
>
>
>
> Many thanks for the info. I did include the resolution as fitting a
> parameter. I will cross check again. BTW, I must have clicked by mistake
> just “reply” button not the “reply to all “.
>
>
>
> Thanks!
>
> Rajesh
>
>
>
> *From:* Dominik Kriegner <dom...@gm...>
> *Sent:* Monday, September 8, 2025 3:41 PM
> *To:* Dutta,Rajesh <rd...@dr...>
> *Subject:* Re: [Xrayutilities-users] thin film roughness
>
>
>
> *External.*
>
> Dear Rajesh,
>
>
>
> There are many reasons these fringes can look different. actually I think
> roughness is somewhat a more unlikely scenario. Roughness will always first
> affect the fringes further away from the main peak.
>
> Other factors which could affect this (but difficult to judge without
> further details):
>
> *) resolution of the measurement. A first hint is the width of the
> substrate peak in measurement vs simulation. but there are also options the
> film signal is more widened due to broadening as compared to the substrate.
> Resolution effects are easy to include in the simulation
>
> *) a strain gradient in the film
>
> *) a composition variation in the film (either lateral or vertical or both)
>
>
>
> kind regards
>
> Dominik
>
>
>
> ps: any reason this can not be discussed on the mailing list where also
> other people benefit?
>
>
>
> On Mon, Sep 8, 2025 at 5:45 PM Dutta,Rajesh <rd...@dr...> wrote:
>
> Hi Dominik,
>
>
>
> Many thanks for the details. I am using simple thin film out-of-plan X-ray
> diffraction. The reason why I am asking is the elongated fringes near 41
> degree which I want to minimize using roughness. See the attached figure
> (it is dynamical fit). It captures everything else nicely. Any tricks to
> reduce those elongated fringes? I can think of about only roughness.
>
>
>
> FYI, I am using simple layer stack, not the pseudomorphic layer. All are
> hexagonal (substrate, film and buffer)
>
>
>
> Thanks!
>
> Rajesh
>
>
>
> *From:* Dominik Kriegner <dom...@gm...>
> *Sent:* Sunday, September 7, 2025 5:27 PM
> *To:* Dutta,Rajesh <rd...@dr...>
> *Cc:* xra...@li...
> *Subject:* Re: [Xrayutilities-users] thin film roughness
>
>
>
> *External.*
>
> Dear Rajesh,
>
>
>
> Please be more specific what kind of data you want to simulate?
> If you refer to simulations of what I call symmetric radial scans (or
> similar) then I have already done this successfully by a weighted sum of
> calculations with layers of different thickness. So basically you loop over
> the full range of thickness values which are possible and average the
> various simulations. Typically I have used a Gaussian distribution of
> weights.
>
> The problem why this can not be done generally or I even did not attempt
> to implement it in xrayutilities is that there are two fundamentally
> different ways to perform the sum. One can imagine a coherent sum (summing
> of electric fields) or an incoherent sum (summing of intensities). These
> two scenarios describe different roughness scenarios, and which should be
> applied depends also on coherence length of the employed radiation. Often
> in reality a mixture of the two methods would be most appropriate.
>
>
>
> Of course none of this is really practical if you have many layers, but
> for few it can work. Note that of course one should then vary the thickness
> of all layers independently which quickly gets numerically demanding.
>
>
>
> kind regards
>
> Dominik Kriegner
>
>
>
> On Sun, Sep 7, 2025 at 10:49 PM Dutta, Rajesh via xrayutilities-users <
> xra...@li...> wrote:
>
> Hi Dominik,
>
>
>
> Is there any way to add surface roughness for XRD simulation in
> xrayutilities?
>
>
>
> Thanks,
>
> Rajesh
>
>
>
>
>
> *-------------------------------------*
>
> *Dr. Rajesh Dutta*
>
>
> *Research Staff Scientist Drexel University College of Engineering
> Pronouns: he/his/him*
>
> Drexel University
> 3100 Market Street
> Philadelphia, PA 19104
> drexel.edu
>
> --------------------------------------------
>
>
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>
>

Re: [Xrayutilities-users] thin film roughness

[Dutta,Rajesh <rd...@dr...>]

Hi Domink,

Many thanks for the info. I did include the resolution as fitting a parameter. I will cross check again. BTW, I must have clicked by mistake just “reply” button not the “reply to all “.

Thanks!
Rajesh

From: Dominik Kriegner <dom...@gm...>
Sent: Monday, September 8, 2025 3:41 PM
To: Dutta,Rajesh <rd...@dr...>
Subject: Re: [Xrayutilities-users] thin film roughness


External.
Dear Rajesh,

There are many reasons these fringes can look different. actually I think roughness is somewhat a more unlikely scenario. Roughness will always first affect the fringes further away from the main peak.
Other factors which could affect this (but difficult to judge without further details):
*) resolution of the measurement. A first hint is the width of the substrate peak in measurement vs simulation. but there are also options the film signal is more widened due to broadening as compared to the substrate. Resolution effects are easy to include in the simulation
*) a strain gradient in the film
*) a composition variation in the film (either lateral or vertical or both)

kind regards
Dominik

ps: any reason this can not be discussed on the mailing list where also other people benefit?

On Mon, Sep 8, 2025 at 5:45 PM Dutta,Rajesh <rd...@dr...<mailto:rd...@dr...>> wrote:
Hi Dominik,

Many thanks for the details. I am using simple thin film out-of-plan X-ray diffraction. The reason why I am asking is the elongated fringes near 41 degree which I want to minimize using roughness. See the attached figure (it is dynamical fit). It captures everything else nicely. Any tricks to reduce those elongated fringes? I can think of about only roughness.

FYI, I am using simple layer stack, not the pseudomorphic layer. All are hexagonal (substrate, film and buffer)

Thanks!
Rajesh
[cid:image001.png@01DC20DD.B5D0BF10]

From: Dominik Kriegner <dom...@gm...<mailto:dom...@gm...>>
Sent: Sunday, September 7, 2025 5:27 PM
To: Dutta,Rajesh <rd...@dr...<mailto:rd...@dr...>>
Cc: xra...@li...<mailto:xra...@li...>
Subject: Re: [Xrayutilities-users] thin film roughness


External.
Dear Rajesh,

Please be more specific what kind of data you want to simulate?
If you refer to simulations of what I call symmetric radial scans (or similar) then I have already done this successfully by a weighted sum of calculations with layers of different thickness. So basically you loop over the full range of thickness values which are possible and average the various simulations. Typically I have used a Gaussian distribution of weights.
The problem why this can not be done generally or I even did not attempt to implement it in xrayutilities is that there are two fundamentally different ways to perform the sum. One can imagine a coherent sum (summing of electric fields) or an incoherent sum (summing of intensities). These two scenarios describe different roughness scenarios, and which should be applied depends also on coherence length of the employed radiation. Often in reality a mixture of the two methods would be most appropriate.

Of course none of this is really practical if you have many layers, but for few it can work. Note that of course one should then vary the thickness of all layers independently which quickly gets numerically demanding.

kind regards
Dominik Kriegner

On Sun, Sep 7, 2025 at 10:49 PM Dutta, Rajesh via xrayutilities-users <xra...@li...<mailto:xra...@li...>> wrote:
Hi Dominik,

Is there any way to add surface roughness for XRD simulation in xrayutilities?

Thanks,
Rajesh


-------------------------------------
Dr. Rajesh Dutta
Research Staff Scientist
Drexel University College of Engineering
Pronouns: he/his/him

Drexel University
3100 Market Street
Philadelphia, PA 19104
drexel.edu<http://drexel.edu/>
--------------------------------------------

_______________________________________________
xrayutilities-users mailing list
xra...@li...<mailto:xra...@li...>
https://lists.sourceforge.net/lists/listinfo/xrayutilities-users

Re: [Xrayutilities-users] thin film roughness

[Dominik K. <dom...@gm...>]

Dear Rajesh,

Please be more specific what kind of data you want to simulate?
If you refer to simulations of what I call symmetric radial scans (or
similar) then I have already done this successfully by a weighted sum of
calculations with layers of different thickness. So basically you loop over
the full range of thickness values which are possible and average the
various simulations. Typically I have used a Gaussian distribution of
weights.
The problem why this can not be done generally or I even did not attempt to
implement it in xrayutilities is that there are two fundamentally different
ways to perform the sum. One can imagine a coherent sum (summing of
electric fields) or an incoherent sum (summing of intensities). These two
scenarios describe different roughness scenarios, and which should be
applied depends also on coherence length of the employed radiation. Often
in reality a mixture of the two methods would be most appropriate.

Of course none of this is really practical if you have many layers, but for
few it can work. Note that of course one should then vary the thickness of
all layers independently which quickly gets numerically demanding.

kind regards
Dominik Kriegner

On Sun, Sep 7, 2025 at 10:49 PM Dutta, Rajesh via xrayutilities-users <
xra...@li...> wrote:

> Hi Dominik,
>
>
>
> Is there any way to add surface roughness for XRD simulation in
> xrayutilities?
>
>
>
> Thanks,
>
> Rajesh
>
>
>
>
>
> *-------------------------------------*
>
> *Dr. Rajesh Dutta*
>
>
> *Research Staff Scientist Drexel University College of Engineering
> Pronouns: he/his/him*
>
> Drexel University
> 3100 Market Street
> Philadelphia, PA 19104
> drexel.edu
>
> --------------------------------------------
>
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>

[Xrayutilities-users] thin film roughness

[Dutta,Rajesh <rd...@dr...>]

Hi Dominik,

Is there any way to add surface roughness for XRD simulation in xrayutilities?

Thanks,
Rajesh


-------------------------------------
Dr. Rajesh Dutta
Research Staff Scientist
Drexel University College of Engineering
Pronouns: he/his/him

Drexel University
3100 Market Street
Philadelphia, PA 19104
drexel.edu<http://drexel.edu/>
--------------------------------------------

Re: [Xrayutilities-users] How to create a "Crystal" out of a "CIFfile"

[Dominik K. <dom...@gm...>]

Dear Maximilian,

It seems to me that a "LayerStack" (which also is automatically created if
you give a list of individual layers to the initialization of the
simulation model) should be good enough.
Indeed for a pseudomorphic stack one needs elastic parameters which are
(unfortunately) never included in the CIF file. One can add them to a
Crystal manually or define the Crystal from scratch with those elastic
parameters if needed. But I understand this is not needed here.

The orientation you want to simulate (which model are you using?) is
typically given to the model initialization via the "Experiment" object.
There could be some pitfalls here with CIFFile since it depends on the
detailed unit cell orientation and it likely was not tested for all
possible (lower symmetry) options.

If there is a cif file and a minimal (not) working example you can share
this would likely help to debug if needed.

kind regards
Dominik

On Tue, Feb 18, 2025 at 9:49 AM Kusch, Maximilian <
max...@he...> wrote:

> Hello Dominik,
>
>
> Thank you for your help! I guess I should have found this myself...
>
> But then maybe I can specify my issue with a follow up question:
>
> I wanted to calculate a XRD of a layered system with materials I extracted
> from a CIFfile. I have seen that the examples use
> xu.simpack.PseudomorphicStack001 to construct such a layer, but this for
> me creates the error that my elastic parameters are zero *"**InputError:
> 'layer' argument needs elastic parameters"* (I guess it is because
> PseudomorphicStack001 makes the in plane lattice parameters matching and
> can't calculate this for my case).
>
> I tried xu.simpack.LayerStack, but this doesn't give me a Bragg peak, i
> think in this method then the information on the orientation of the crystal
> is missing.
>
> If i just want to have layers of these two materials leaving the lattice
> parameters independent from each other (knowing that this is unphysical),
> but want to have the orientation specified to get the (0 0 l) Bragg peak,
> is then CrystalStack the method of choice? And how do I specify the
> orientation of the two materials?
>
>
> Thank you very much for you help!
>
> Maximilian Kusch
>
>
> ------------------------------
> *Von:* Dominik Kriegner <dom...@gm...>
> *Gesendet:* Montag, 17. Februar 2025 21:48:01
> *An:* Kusch, Maximilian
> *Cc:* xra...@li...
> *Betreff:* Re: [Xrayutilities-users] How to create a "Crystal" out of a
> "CIFfile"
>
> Hello,
>
> There is a function called Crystal.fromCIF which can directly create a
> crystal object corresponding to the default entry in the CIF file.
> This is the most straightforward way. The source of that function (3
> lines) can also inspire you to do it manually from a CIFFile object.
>
>
> https://xrayutilities.sourceforge.io/xrayutilities.materials.html#xrayutilities.materials.material.Crystal.fromCIF
>
> Cheers
> Dominik
>
> On Mon, Feb 17, 2025 at 3:11 PM Kusch, Maximilian <
> max...@he...> wrote:
>
>> Dear all,
>>
>>
>> What is in the current version of xrayutilities the easiest way to create
>> a xrayutilities.materials.material.Crystal
>>
>> out of a xrayutilities.materials.cif.CIFFile, which only has the methods
>> Parse() and SGLattice()
>>
>>
>> thank you very much for your help
>>
>> Maximilian Kusch
>>
>> ------------------------------
>>
>> Helmholtz-Zentrum Berlin für Materialien und Energie GmbH
>>
>> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher
>> Forschungszentren e.V.
>>
>> Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta
>> Koch-Unterseher
>> Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking
>>
>> Sitz Berlin, AG Charlottenburg, 89 HRB 5583
>>
>> Postadresse:
>> Hahn-Meitner-Platz 1
>> 14109 Berlin
>> Deutschland
>>
>> Diese E-Mail kann vertrauliche und/oder rechtlich geschützte
>> Informationen enthalten. Wenn Sie diese E-Mail irrtümlich erhalten haben,
>> informieren Sie bitte sofort den*die Absender*in und vernichten Sie diese
>> Mail. Das unerlaubte Kopieren, die Veröffentlichung sowie die unbefugte
>> Weitergabe dieser Mail ist nicht gestattet.
>> This email may contain confidential and/or proprietary information. If
>> you have received this e-mail in error, please inform the sender
>> immediately and destroy this e-mail. Unauthorized copying, publishing or
>> distribution of this e-mail is not permitted.
>> _______________________________________________
>> xrayutilities-users mailing list
>> xra...@li...
>> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>>
>
> ------------------------------
>
> Helmholtz-Zentrum Berlin für Materialien und Energie GmbH
>
> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher
> Forschungszentren e.V.
>
> Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta
> Koch-Unterseher
> Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking
>
> Sitz Berlin, AG Charlottenburg, 89 HRB 5583
>
> Postadresse:
> Hahn-Meitner-Platz 1
> 14109 Berlin
> Deutschland
>
> Diese E-Mail kann vertrauliche und/oder rechtlich geschützte Informationen
> enthalten. Wenn Sie diese E-Mail irrtümlich erhalten haben, informieren Sie
> bitte sofort den*die Absender*in und vernichten Sie diese Mail. Das
> unerlaubte Kopieren, die Veröffentlichung sowie die unbefugte Weitergabe
> dieser Mail ist nicht gestattet.
> This email may contain confidential and/or proprietary information. If you
> have received this e-mail in error, please inform the sender immediately
> and destroy this e-mail. Unauthorized copying, publishing or distribution
> of this e-mail is not permitted.
>

Re: [Xrayutilities-users] How to create a "Crystal" out of a "CIFfile"

[Kusch, M. <max...@he...>]

Hello Dominik,


Thank you for your help! I guess I should have found this myself...

But then maybe I can specify my issue with a follow up question:

I wanted to calculate a XRD of a layered system with materials I extracted from a CIFfile. I have seen that the examples use xu.simpack.PseudomorphicStack001 to construct such a layer, but this for me creates the error that my elastic parameters are zero "InputError: 'layer' argument needs elastic parameters" (I guess it is because PseudomorphicStack001 makes the in plane lattice parameters matching and can't calculate this for my case).

I tried xu.simpack.LayerStack, but this doesn't give me a Bragg peak, i think in this method then the information on the orientation of the crystal is missing.

If i just want to have layers of these two materials leaving the lattice parameters independent from each other (knowing that this is unphysical), but want to have the orientation specified to get the (0 0 l) Bragg peak, is then CrystalStack the method of choice? And how do I specify the orientation of the two materials?


Thank you very much for you help!

Maximilian Kusch


________________________________
Von: Dominik Kriegner <dom...@gm...>
Gesendet: Montag, 17. Februar 2025 21:48:01
An: Kusch, Maximilian
Cc: xra...@li...
Betreff: Re: [Xrayutilities-users] How to create a "Crystal" out of a "CIFfile"

Hello,

There is a function called Crystal.fromCIF which can directly create a crystal object corresponding to the default entry in the CIF file.
This is the most straightforward way. The source of that function (3 lines) can also inspire you to do it manually from a CIFFile object.

https://xrayutilities.sourceforge.io/xrayutilities.materials.html#xrayutilities.materials.material.Crystal.fromCIF

Cheers
Dominik

On Mon, Feb 17, 2025 at 3:11 PM Kusch, Maximilian <max...@he...<mailto:max...@he...>> wrote:

Dear all,


What is in the current version of xrayutilities the easiest way to create a xrayutilities.materials.material.Crystal

out of a xrayutilities.materials.cif.CIFFile, which only has the methods Parse() and SGLattice()


thank you very much for your help

Maximilian Kusch

________________________________

Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland

Diese E-Mail kann vertrauliche und/oder rechtlich geschützte Informationen enthalten. Wenn Sie diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den*die Absender*in und vernichten Sie diese Mail. Das unerlaubte Kopieren, die Veröffentlichung sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet.
This email may contain confidential and/or proprietary information. If you have received this e-mail in error, please inform the sender immediately and destroy this e-mail. Unauthorized copying, publishing or distribution of this e-mail is not permitted.
_______________________________________________
xrayutilities-users mailing list
xra...@li...<mailto:xra...@li...>
https://lists.sourceforge.net/lists/listinfo/xrayutilities-users

________________________________

Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland

Diese E-Mail kann vertrauliche und/oder rechtlich geschützte Informationen enthalten. Wenn Sie diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den*die Absender*in und vernichten Sie diese Mail. Das unerlaubte Kopieren, die Veröffentlichung sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet.
This email may contain confidential and/or proprietary information. If you have received this e-mail in error, please inform the sender immediately and destroy this e-mail. Unauthorized copying, publishing or distribution of this e-mail is not permitted.

Re: [Xrayutilities-users] How to create a "Crystal" out of a "CIFfile"

[Dominik K. <dom...@gm...>]

Hello,

There is a function called Crystal.fromCIF which can directly create a
crystal object corresponding to the default entry in the CIF file.
This is the most straightforward way. The source of that function (3 lines)
can also inspire you to do it manually from a CIFFile object.

https://xrayutilities.sourceforge.io/xrayutilities.materials.html#xrayutilities.materials.material.Crystal.fromCIF

Cheers
Dominik

On Mon, Feb 17, 2025 at 3:11 PM Kusch, Maximilian <
max...@he...> wrote:

> Dear all,
>
>
> What is in the current version of xrayutilities the easiest way to create
> a xrayutilities.materials.material.Crystal
>
> out of a xrayutilities.materials.cif.CIFFile, which only has the methods
> Parse() and SGLattice()
>
>
> thank you very much for your help
>
> Maximilian Kusch
>
> ------------------------------
>
> Helmholtz-Zentrum Berlin für Materialien und Energie GmbH
>
> Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher
> Forschungszentren e.V.
>
> Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta
> Koch-Unterseher
> Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking
>
> Sitz Berlin, AG Charlottenburg, 89 HRB 5583
>
> Postadresse:
> Hahn-Meitner-Platz 1
> 14109 Berlin
> Deutschland
>
> Diese E-Mail kann vertrauliche und/oder rechtlich geschützte Informationen
> enthalten. Wenn Sie diese E-Mail irrtümlich erhalten haben, informieren Sie
> bitte sofort den*die Absender*in und vernichten Sie diese Mail. Das
> unerlaubte Kopieren, die Veröffentlichung sowie die unbefugte Weitergabe
> dieser Mail ist nicht gestattet.
> This email may contain confidential and/or proprietary information. If you
> have received this e-mail in error, please inform the sender immediately
> and destroy this e-mail. Unauthorized copying, publishing or distribution
> of this e-mail is not permitted.
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>

[Xrayutilities-users] How to create a "Crystal" out of a "CIFfile"

[Kusch, M. <max...@he...>]

Dear all,


What is in the current version of xrayutilities the easiest way to create a xrayutilities.materials.material.Crystal

out of a xrayutilities.materials.cif.CIFFile, which only has the methods Parse() and SGLattice()


thank you very much for your help

Maximilian Kusch

________________________________

Helmholtz-Zentrum Berlin für Materialien und Energie GmbH

Mitglied der Hermann von Helmholtz-Gemeinschaft Deutscher Forschungszentren e.V.

Aufsichtsrat: Vorsitzender Dr. Volkmar Dietz, stv. Vorsitzende Dr. Jutta Koch-Unterseher
Geschäftsführung: Prof. Dr. Bernd Rech, Thomas Frederking

Sitz Berlin, AG Charlottenburg, 89 HRB 5583

Postadresse:
Hahn-Meitner-Platz 1
14109 Berlin
Deutschland

Diese E-Mail kann vertrauliche und/oder rechtlich geschützte Informationen enthalten. Wenn Sie diese E-Mail irrtümlich erhalten haben, informieren Sie bitte sofort den*die Absender*in und vernichten Sie diese Mail. Das unerlaubte Kopieren, die Veröffentlichung sowie die unbefugte Weitergabe dieser Mail ist nicht gestattet.
This email may contain confidential and/or proprietary information. If you have received this e-mail in error, please inform the sender immediately and destroy this e-mail. Unauthorized copying, publishing or distribution of this e-mail is not permitted.

Re: [Xrayutilities-users] hxrd.Ang2Q and Ang2HKL running in parallel

[Dominik K. <dom...@gm...>]

Dear Carsten,

yes this behavior is expected. It can also be configured.

The config option 'NTHREADS' should allow you to control it. [1]
If you want the full package to run without parallelization you can also
consider to build the library without the openmp support. There is a note
about this in the install section [2] of the readme. (Unfortunately this is
not included in the documentation webpage).

hope this helps.

cheers
Dominik

[1]
https://github.com/dkriegner/xrayutilities/blob/8a0e206ee538399ff9ea2ff78740ee09b3e0785f/lib/xrayutilities/xrayutilities_default.conf#L29
[2]
https://github.com/dkriegner/xrayutilities/tree/main?tab=readme-ov-file#installation-source

On Mon, Sep 30, 2024 at 9:17 AM Richter, Dr. Carsten <
car...@ik...> wrote:

>
> Dear all,
>
>
>
> the methods hxrd.Ang2HKL and hxrd.Ang2Q are intrinsically running in
> parallel on our cluster:
>
>
>
> …
>
> %%timeit -n 2000
>
> hxrd.Ang2HKL(30, 0, 0, 60, 0)
>
> …
>
>
>
>    PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+
> COMMAND
>
>
> 107379 richter   20   0 2554528 159352  30272 R  1466  0.1   8:05.20
> python
>
>
>
>
>
>
> Is this behavior expected? Is there any way to control it?
>
>
>
> Best regards
>
> Carsten
>
>
>
> =================================
>
>
>
> Leibniz-Institut für Kristallzüchtung (IKZ)
>
> https://www.ikz-berlin.de
>
> Max Born Str. 2
>
> 12489 Berlin / Germany
>
>
>
> Phone: +49 30 6392 2859
>
>
>
> ------------------------------
>
> Dr. Carsten Richter
> Nachwuchsgruppenleiter X-Ray Imaging
> Materialwissenschaften/Experimentelle Charakterisierung
> T: +49 (0)30 6392 2859
> F: +49 (0)30 6392 3003
> E: car...@ik...
>
> Diese Nachricht enthält vertrauliche Informationen und ist nur für die
> genannten Empfänger bestimmt. Falls Sie kein genannter Empfänger sind,
> dürfen Sie diese E-Mail nicht verbreiten, verteilen oder kopieren. Bitte
> benachrichtigen Sie car...@ik... umgehend per E-Mail,
> falls Sie diese E-Mail fälschlicherweise erhalten haben, und löschen Sie
> sie von lhrem System. Eine sichere und fehlerfreie E-Mail-Übertragung kann
> nicht gewährleistet werden, da Informationen abgefangen, beschädigt,
> zerstört, verzögert werden, verloren gehen, unvollständig sein oder Viren
> enthalten können. Aus diesem Grund übernimmt Leibniz-Institut für
> Kristallzüchtung (IKZ) im FVB e.V. keine Haftung für jedwede Fehler oder
> Auslassungen in dieser Nachricht, die auf eine E-Mail-Übertragung
> zurückzuführen sind. Falls eine Bestätigung erforderlich ist, fordern Sie
> bitte eine gedruckte Version an.
>
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>

[Xrayutilities-users] hxrd.Ang2Q and Ang2HKL running in parallel

[Richter, D. C. <car...@ik...>]

Dear all,

the methods hxrd.Ang2HKL and hxrd.Ang2Q are intrinsically running in parallel on our cluster:

…
%%timeit -n 2000
hxrd.Ang2HKL(30, 0, 0, 60, 0)
…

   PID USER      PR  NI    VIRT    RES    SHR S  %CPU %MEM     TIME+ COMMAND
107379 richter   20   0 2554528 159352  30272 R  1466  0.1   8:05.20 python


Is this behavior expected? Is there any way to control it?

Best regards
Carsten

=================================

Leibniz-Institut für Kristallzüchtung (IKZ)
https://www.ikz-berlin.de
Max Born Str. 2
12489 Berlin / Germany

Phone: +49 30 6392 2859


________________________________
Dr. Carsten Richter
Nachwuchsgruppenleiter X-Ray Imaging
Materialwissenschaften/Experimentelle Charakterisierung
T: +49 (0)30 6392 2859
F: +49 (0)30 6392 3003
E: car...@ik...<mailto:car...@ik...>


[cid:image2cd454.PNG@2bfb53e3.4db8a456]
LEIBNIZ-INSTITUT
FÜR KRISTALLZÜCHTUNG
im Forschungsverbund Berlin e.V.

Max-Born-Straße 2
12489 Berlin
www.ikz-berlin.de<https://www.ikz-berlin.de/>

________________________________

Diese Nachricht enthält vertrauliche Informationen und ist nur für die genannten Empfänger bestimmt. Falls Sie kein genannter Empfänger sind, dürfen Sie diese E-Mail nicht verbreiten, verteilen oder kopieren. Bitte benachrichtigen Sie car...@ik... umgehend per E-Mail, falls Sie diese E-Mail fälschlicherweise erhalten haben, und löschen Sie sie von lhrem System. Eine sichere und fehlerfreie E-Mail-Übertragung kann nicht gewährleistet werden, da Informationen abgefangen, beschädigt, zerstört, verzögert werden, verloren gehen, unvollständig sein oder Viren enthalten können. Aus diesem Grund übernimmt Leibniz-Institut für Kristallzüchtung (IKZ) im FVB e.V. keine Haftung für jedwede Fehler oder Auslassungen in dieser Nachricht, die auf eine E-Mail-Übertragung zurückzuführen sind. Falls eine Bestätigung erforderlich ist, fordern Sie bitte eine gedruckte Version an.

Re: [Xrayutilities-users] XRD-Simulation needs elastic parameters

[Dominik K. <dom...@gm...>]

Dear all,

Regarding the data import of RAS files xrayutilities I see nothing wrong
with it.
The data object contains three columns. If you plot only intensity then
this is exactly what you get: the real measured intensity which one can
also use to obtain the error bar from counting statistics. You have to
multiply with the attenuation factor to get the corrected intensity. I
believe this makes sense like this.

kind regards
Dominik

On Sat, Aug 24, 2024 at 7:20 AM Dutta, Rajesh via xrayutilities-users <
xra...@li...> wrote:

> Dear Paritosh,
>
>
>
> Thanks for your effort and time, I appreciate it. There is no experimental
> fault for the substrate peak. This was importing problem of xrayutitlities
> itself. Please see the attached picture for clarity. If I just plot using
> the raw data, it is fine. I found where the problem is. In the .ras file
> there are three columns: 2theta, counts and attenuator normalization
> factor. If you look the third column (attached) they are normalized with
> the number around 45. When we plot, we need to multiply column 2 and 3 to
> get the total counts. I guess, this is not included in xrayutilities and
> this is why we see three bumbs if you just plot 2nd cloumn. I already
> informed Dominik about this.
>
>
>
> Regarding the second strong peak, yes, they are coming from different
> domain and the fringes are suppressed because of it’s higher thickness
> nearly 100 nm and also probably bit rough.
>
>
>
> Regards,
>
> Rajesh
>
>
>
> *From:* Paritosh Wadekar <par...@gm...>
> *Sent:* Friday, August 23, 2024 4:57 PM
> *To:* Dutta,Rajesh <rd...@dr...>
> *Subject:* Re: [Xrayutilities-users] XRD-Simulation needs elastic
> parameters
>
>
>
> *External.*
>
> Thanks for the clarification.  Well attached is a ppt with some of my
> thoughts about your experimental data. Totally up to you if you want to use
> it or not.
>
> Regards
>
> Paritosh
>
>
> [image: Image removed by sender.]
>
> On Sat, Aug 24, 2024 at 2:56 AM Dutta,Rajesh <rd...@dr...> wrote:
>
> Hi Paritosh,
>
>
>
> No, it was MBE.
>
>
>
> Thanks, Rajesh
>
>
>
> *From:* Paritosh Wadekar <par...@gm...>
> *Sent:* Friday, August 23, 2024 5:51 AM
> *To:* Dutta,Rajesh <rd...@dr...>
> *Cc:* Dominik Kriegner <dom...@gm...>;
> xra...@li...
> *Subject:* Re: [Xrayutilities-users] XRD-Simulation needs elastic
> parameters
>
>
>
> *External.*
>
> Hello Rajesh,
>
> Interesting fittings but if I am right you have deposited your thin films
> using pulsed laser deposition right ?
>
> Paritosh
>
>
>
> On Fri, Aug 23, 2024, 6:18 PM Dutta, Rajesh via xrayutilities-users <
> xra...@li...> wrote:
>
> Dear Dominik,
>
>
>
> Many thanks for the fruitful hints. It is doable somehow even though it is
> orthorhombic system on top of cubic. Luckily, our SrFeO2.5 (5.6, 5.65,
> 15.7A) can be treated as pseudocubic system (rotating 45 deg around
> c-axis). With this setting a,b axes of SrFeO2.5 become like cubic
> SrTiO3(3.905A). However, I had to manually build both the SrTiO3 and
> SrFeO2.5 to match the c-axis and to incorporate elastic constants as well.
> Please have a look at the attached figure (simulation and experimental
> data). Let me know your thoughts.
>
>
>
> Besides that, I have questions: (1) Only multibeam kinematical model takes
> all the reflections using “surface_hkl=(0,0,1)” where others take only one
> given (H, K, L). Is there any way to make a list for (H,K,L) so that other
> model can calculate the XRD for several (H,K,L). I tried to give a list but
> did not work. (2) Is the relaxation parameter treated as strain/stress
> here? If not, how can I input in-plane stress or strain? I will try to fit
> the data and let you know the outcomes.
>
>
>
> Thanks again,
>
> Bye,
>
> Rajesh
>
>
>
> *From:* Dominik Kriegner <dom...@gm...>
> *Sent:* Thursday, August 22, 2024 5:46 AM
> *To:* Dutta,Rajesh <rd...@dr...>
> *Cc:* xra...@li...
> *Subject:* Re: [Xrayutilities-users] XRD-Simulation needs elastic
> parameters
>
>
>
> *External.*
>
> Dear Rajesh,
>
>
>
> Is there a standardized way the elastic parameters are provided in the cif
> files? If so one could update the parser to allow to read it properly.
>
>
>
> But likely it's better you define the materials manually. I recommend you
> to look at
>
> https://xrayutilities
> .sourceforge.io/examples.html#using-the-materials-subpackage
>
> I am however afraid I did not include some documentation on how to add the
> elastic parameters. For this maybe best look at how it is done for the
> predefined materials in the code
>
> https://github.com/dkriegner/xrayutilities/blob/main/lib/xrayutilities
> /materials/predefined_materials.py
>
>
>
> Finally I must warn you that I do believe that the pseudomorphic stack was
> never tested for orthorhombic materials on top of a cubic material. I am
> almost certain it won't exactly do what you expect.
>
> You might be able to help yourself and distort the material as you see
> fit, but I would not rely on the pseudomorphicstack code to work without
> changes!
>
>
>
> cheers
>
> Dominik
>
>
>
> On Thu, Aug 22, 2024 at 2:21 AM Dutta, Rajesh via xrayutilities-users <
> xra...@li...> wrote:
>
> Dear xrayutilities users,
>
>
>
> I am very new to this tool. I am trying to build a layer stack of Sr2Fe2O5
> (ortho) on top of SrTiO3 substrate (cubic). I managed to construct the
> model using cif files. However, in the cif file seemingly it is not
> possible to incorporate cij (elastic parameters). Therefore, the fitting
> XRD gives an error saying “layer’ argument needs elastic parameters.
>
>
>
> How to solve this issue while importing cif files. I attach few parts of
> the code below:
>
>
>
> # global parameters
>
> wavelength = xu.wavelength('CuKa1')
>
> offset = -0.00  # angular offset of the zero position of the data
>
>
>
> # set up LayerStack for simulation: SrTiO3/SrFeO2.5
>
> Sr = xu.materials.elements.Sr <http://xu.materials.elements.sr/>
>
> Ti = xu.materials.elements.Ti
>
> O = xu.materials.elements.O
>
> Fe = xu.materials.elements.Fe
>
> STO = xu.materials.Crystal.fromCIF(os.path.join("data", "STO.cif"))
>
> SFO = xu.materials.Crystal.fromCIF(os.path.join("data",
> "Sr2Fe2O5-along.cif"))
>
>
>
> lSTO = xu.simpack.Layer(STO, inf)
>
> lSFO = xu.simpack.Layer(SFO, 800, relaxation=0)
>
>
>
> pstack = xu.simpack.PseudomorphicStack001('list', lSTO, lSFO)
>
>
>
> # set up simulation object
>
> thetaMono = arcsin(wavelength/(2 * xu.materials.Ge.planeDistance(2, 2, 0)))
>
> Cmono = cos(2 * thetaMono)
>
> dyn = xu.simpack.DynamicalModel(pstack, I0=1.5e5, background=0,
>
>                                 resolution_width=2e-3, polarization='both',
>
>                                 Cmono=Cmono)
>
> fitmdyn = xu.simpack.FitModel(dyn)
>
> fitmdyn.set_param_hint('SFO_a', vary=True, min=15.7, max=15.8)
>
> fitmdyn.set_param_hint('STO_a', vary=True, min=3.90, max=3.91)
>
> fitmdyn.set_param_hint('resolution_width', vary=True)
>
> params = fitmdyn.make_params()
>
>
>
> I tried to build the materials using Crystal class and SGLattice, there I
> can define elastic tensors but it does not account proper Wyckoff
> positions, this is why I used cif files.
>
>
>
> Any help, please let me know if you need more info.
>
>
>
> Thanks,
>
> Rajesh
>
>
>
> *-------------------------------------*
>
> *Dr. Rajesh Dutta*
>
>
> *Research Staff Scientist Drexel University College of Engineering
> Pronouns: he/his/him*
>
> Drexel University
> 3100 Market Street
> <https://www.google.com/maps/search/3100+Market+Street+%0D%0APhiladelphia,+PA+19104?entry=gmail&source=g>
> Philadelphia, PA 19104
> <https://www.google.com/maps/search/3100+Market+Street+%0D%0APhiladelphia,+PA+19104?entry=gmail&source=g>
> drexel.edu
>
> --------------------------------------------
>
>
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>
>
>
>
> --
>
>
>
> *Dr Paritosh Wadekar*
>
>
>
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>

Re: [Xrayutilities-users] XRD-Simulation needs elastic parameters

[Dutta,Rajesh <rd...@dr...>]

Dear Paritosh,

Thanks for your effort and time, I appreciate it. There is no experimental fault for the substrate peak. This was importing problem of xrayutitlities itself. Please see the attached picture for clarity. If I just plot using the raw data, it is fine. I found where the problem is. In the .ras file there are three columns: 2theta, counts and attenuator normalization factor. If you look the third column (attached) they are normalized with the number around 45. When we plot, we need to multiply column 2 and 3 to get the total counts. I guess, this is not included in xrayutilities and this is why we see three bumbs if you just plot 2nd cloumn. I already informed Dominik about this.

Regarding the second strong peak, yes, they are coming from different domain and the fringes are suppressed because of it’s higher thickness nearly 100 nm and also probably bit rough.

Regards,
Rajesh

From: Paritosh Wadekar <par...@gm...>
Sent: Friday, August 23, 2024 4:57 PM
To: Dutta,Rajesh <rd...@dr...>
Subject: Re: [Xrayutilities-users] XRD-Simulation needs elastic parameters


External.
Thanks for the clarification.  Well attached is a ppt with some of my thoughts about your experimental data. Totally up to you if you want to use it or not.
Regards
Paritosh

[Image removed by sender.]
On Sat, Aug 24, 2024 at 2:56 AM Dutta,Rajesh <rd...@dr...<mailto:rd...@dr...>> wrote:
Hi Paritosh,

No, it was MBE.

Thanks, Rajesh

From: Paritosh Wadekar <par...@gm...<mailto:par...@gm...>>
Sent: Friday, August 23, 2024 5:51 AM
To: Dutta,Rajesh <rd...@dr...<mailto:rd...@dr...>>
Cc: Dominik Kriegner <dom...@gm...<mailto:dom...@gm...>>; xra...@li...<mailto:xra...@li...>
Subject: Re: [Xrayutilities-users] XRD-Simulation needs elastic parameters


External.
Hello Rajesh,
Interesting fittings but if I am right you have deposited your thin films using pulsed laser deposition right ?
Paritosh

On Fri, Aug 23, 2024, 6:18 PM Dutta, Rajesh via xrayutilities-users <xra...@li...<mailto:xra...@li...>> wrote:
Dear Dominik,

Many thanks for the fruitful hints. It is doable somehow even though it is orthorhombic system on top of cubic. Luckily, our SrFeO2.5 (5.6, 5.65, 15.7A) can be treated as pseudocubic system (rotating 45 deg around c-axis). With this setting a,b axes of SrFeO2.5 become like cubic SrTiO3(3.905A). However, I had to manually build both the SrTiO3 and SrFeO2.5 to match the c-axis and to incorporate elastic constants as well. Please have a look at the attached figure (simulation and experimental data). Let me know your thoughts.

Besides that, I have questions: (1) Only multibeam kinematical model takes all the reflections using “surface_hkl=(0,0,1)” where others take only one given (H, K, L). Is there any way to make a list for (H,K,L) so that other model can calculate the XRD for several (H,K,L). I tried to give a list but did not work. (2) Is the relaxation parameter treated as strain/stress here? If not, how can I input in-plane stress or strain? I will try to fit the data and let you know the outcomes.

Thanks again,
Bye,
Rajesh

From: Dominik Kriegner <dom...@gm...<mailto:dom...@gm...>>
Sent: Thursday, August 22, 2024 5:46 AM
To: Dutta,Rajesh <rd...@dr...<mailto:rd...@dr...>>
Cc: xra...@li...<mailto:xra...@li...>
Subject: Re: [Xrayutilities-users] XRD-Simulation needs elastic parameters


External.
Dear Rajesh,

Is there a standardized way the elastic parameters are provided in the cif files? If so one could update the parser to allow to read it properly.

But likely it's better you define the materials manually. I recommend you to look at
https://xrayutilities.sourceforge.io/examples.html#using-the-materials-subpackage
I am however afraid I did not include some documentation on how to add the elastic parameters. For this maybe best look at how it is done for the predefined materials in the code
https://github.com/dkriegner/xrayutilities/blob/main/lib/xrayutilities/materials/predefined_materials.py

Finally I must warn you that I do believe that the pseudomorphic stack was never tested for orthorhombic materials on top of a cubic material. I am almost certain it won't exactly do what you expect.
You might be able to help yourself and distort the material as you see fit, but I would not rely on the pseudomorphicstack code to work without changes!

cheers
Dominik

On Thu, Aug 22, 2024 at 2:21 AM Dutta, Rajesh via xrayutilities-users <xra...@li...<mailto:xra...@li...>> wrote:
Dear xrayutilities users,

I am very new to this tool. I am trying to build a layer stack of Sr2Fe2O5 (ortho) on top of SrTiO3 substrate (cubic). I managed to construct the model using cif files. However, in the cif file seemingly it is not possible to incorporate cij (elastic parameters). Therefore, the fitting XRD gives an error saying “layer’ argument needs elastic parameters.

How to solve this issue while importing cif files. I attach few parts of the code below:

# global parameters
wavelength = xu.wavelength('CuKa1')
offset = -0.00  # angular offset of the zero position of the data

# set up LayerStack for simulation: SrTiO3/SrFeO2.5
Sr = xu.materials.elements.Sr<http://xu.materials.elements.sr/>
Ti = xu.materials.elements.Ti
O = xu.materials.elements.O
Fe = xu.materials.elements.Fe
STO = xu.materials.Crystal.fromCIF(os.path.join("data", "STO.cif"))
SFO = xu.materials.Crystal.fromCIF(os.path.join("data", "Sr2Fe2O5-along.cif"))

lSTO = xu.simpack.Layer(STO, inf)
lSFO = xu.simpack.Layer(SFO, 800, relaxation=0)

pstack = xu.simpack.PseudomorphicStack001('list', lSTO, lSFO)

# set up simulation object
thetaMono = arcsin(wavelength/(2 * xu.materials.Ge.planeDistance(2, 2, 0)))
Cmono = cos(2 * thetaMono)
dyn = xu.simpack.DynamicalModel(pstack, I0=1.5e5, background=0,
                                resolution_width=2e-3, polarization='both',
                                Cmono=Cmono)
fitmdyn = xu.simpack.FitModel(dyn)
fitmdyn.set_param_hint('SFO_a', vary=True, min=15.7, max=15.8)
fitmdyn.set_param_hint('STO_a', vary=True, min=3.90, max=3.91)
fitmdyn.set_param_hint('resolution_width', vary=True)
params = fitmdyn.make_params()

I tried to build the materials using Crystal class and SGLattice, there I can define elastic tensors but it does not account proper Wyckoff positions, this is why I used cif files.

Any help, please let me know if you need more info.

Thanks,
Rajesh

-------------------------------------
Dr. Rajesh Dutta
Research Staff Scientist
Drexel University College of Engineering
Pronouns: he/his/him

Drexel University
3100 Market Street<https://www.google.com/maps/search/3100+Market+Street+%0D%0APhiladelphia,+PA+19104?entry=gmail&source=g>
Philadelphia, PA 19104<https://www.google.com/maps/search/3100+Market+Street+%0D%0APhiladelphia,+PA+19104?entry=gmail&source=g>
drexel.edu<http://drexel.edu/>
--------------------------------------------

_______________________________________________
xrayutilities-users mailing list
xra...@li...<mailto:xra...@li...>
https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
_______________________________________________
xrayutilities-users mailing list
xra...@li...<mailto:xra...@li...>
https://lists.sourceforge.net/lists/listinfo/xrayutilities-users


--

Dr Paritosh Wadekar

Re: [Xrayutilities-users] XRD-Simulation needs elastic parameters

[Paritosh W. <par...@gm...>]

Hello Rajesh,
Interesting fittings but if I am right you have deposited your thin films
using pulsed laser deposition right ?
Paritosh

On Fri, Aug 23, 2024, 6:18 PM Dutta, Rajesh via xrayutilities-users <
xra...@li...> wrote:

> Dear Dominik,
>
>
>
> Many thanks for the fruitful hints. It is doable somehow even though it is
> orthorhombic system on top of cubic. Luckily, our SrFeO2.5 (5.6, 5.65,
> 15.7A) can be treated as pseudocubic system (rotating 45 deg around
> c-axis). With this setting a,b axes of SrFeO2.5 become like cubic
> SrTiO3(3.905A). However, I had to manually build both the SrTiO3 and
> SrFeO2.5 to match the c-axis and to incorporate elastic constants as well.
> Please have a look at the attached figure (simulation and experimental
> data). Let me know your thoughts.
>
>
>
> Besides that, I have questions: (1) Only multibeam kinematical model takes
> all the reflections using “surface_hkl=(0,0,1)” where others take only one
> given (H, K, L). Is there any way to make a list for (H,K,L) so that other
> model can calculate the XRD for several (H,K,L). I tried to give a list but
> did not work. (2) Is the relaxation parameter treated as strain/stress
> here? If not, how can I input in-plane stress or strain? I will try to fit
> the data and let you know the outcomes.
>
>
>
> Thanks again,
>
> Bye,
>
> Rajesh
>
>
>
> *From:* Dominik Kriegner <dom...@gm...>
> *Sent:* Thursday, August 22, 2024 5:46 AM
> *To:* Dutta,Rajesh <rd...@dr...>
> *Cc:* xra...@li...
> *Subject:* Re: [Xrayutilities-users] XRD-Simulation needs elastic
> parameters
>
>
>
> *External.*
>
> Dear Rajesh,
>
>
>
> Is there a standardized way the elastic parameters are provided in the cif
> files? If so one could update the parser to allow to read it properly.
>
>
>
> But likely it's better you define the materials manually. I recommend you
> to look at
>
> https://xrayutilities
> .sourceforge.io/examples.html#using-the-materials-subpackage
>
> I am however afraid I did not include some documentation on how to add the
> elastic parameters. For this maybe best look at how it is done for the
> predefined materials in the code
>
> https://github.com/dkriegner/xrayutilities/blob/main/lib/xrayutilities
> /materials/predefined_materials.py
>
>
>
> Finally I must warn you that I do believe that the pseudomorphic stack was
> never tested for orthorhombic materials on top of a cubic material. I am
> almost certain it won't exactly do what you expect.
>
> You might be able to help yourself and distort the material as you see
> fit, but I would not rely on the pseudomorphicstack code to work without
> changes!
>
>
>
> cheers
>
> Dominik
>
>
>
> On Thu, Aug 22, 2024 at 2:21 AM Dutta, Rajesh via xrayutilities-users <
> xra...@li...> wrote:
>
> Dear xrayutilities users,
>
>
>
> I am very new to this tool. I am trying to build a layer stack of Sr2Fe2O5
> (ortho) on top of SrTiO3 substrate (cubic). I managed to construct the
> model using cif files. However, in the cif file seemingly it is not
> possible to incorporate cij (elastic parameters). Therefore, the fitting
> XRD gives an error saying “layer’ argument needs elastic parameters.
>
>
>
> How to solve this issue while importing cif files. I attach few parts of
> the code below:
>
>
>
> # global parameters
>
> wavelength = xu.wavelength('CuKa1')
>
> offset = -0.00  # angular offset of the zero position of the data
>
>
>
> # set up LayerStack for simulation: SrTiO3/SrFeO2.5
>
> Sr = xu.materials.elements.Sr <http://xu.materials.elements.sr/>
>
> Ti = xu.materials.elements.Ti
>
> O = xu.materials.elements.O
>
> Fe = xu.materials.elements.Fe
>
> STO = xu.materials.Crystal.fromCIF(os.path.join("data", "STO.cif"))
>
> SFO = xu.materials.Crystal.fromCIF(os.path.join("data",
> "Sr2Fe2O5-along.cif"))
>
>
>
> lSTO = xu.simpack.Layer(STO, inf)
>
> lSFO = xu.simpack.Layer(SFO, 800, relaxation=0)
>
>
>
> pstack = xu.simpack.PseudomorphicStack001('list', lSTO, lSFO)
>
>
>
> # set up simulation object
>
> thetaMono = arcsin(wavelength/(2 * xu.materials.Ge.planeDistance(2, 2, 0)))
>
> Cmono = cos(2 * thetaMono)
>
> dyn = xu.simpack.DynamicalModel(pstack, I0=1.5e5, background=0,
>
>                                 resolution_width=2e-3, polarization='both',
>
>                                 Cmono=Cmono)
>
> fitmdyn = xu.simpack.FitModel(dyn)
>
> fitmdyn.set_param_hint('SFO_a', vary=True, min=15.7, max=15.8)
>
> fitmdyn.set_param_hint('STO_a', vary=True, min=3.90, max=3.91)
>
> fitmdyn.set_param_hint('resolution_width', vary=True)
>
> params = fitmdyn.make_params()
>
>
>
> I tried to build the materials using Crystal class and SGLattice, there I
> can define elastic tensors but it does not account proper Wyckoff
> positions, this is why I used cif files.
>
>
>
> Any help, please let me know if you need more info.
>
>
>
> Thanks,
>
> Rajesh
>
>
>
> *-------------------------------------*
>
> *Dr. Rajesh Dutta*
>
>
> *Research Staff Scientist Drexel University College of Engineering
> Pronouns: he/his/him*
>
> Drexel University
> 3100 Market Street
> <https://www.google.com/maps/search/3100+Market+Street+%0D%0APhiladelphia,+PA+19104?entry=gmail&source=g>
> Philadelphia, PA 19104
> <https://www.google.com/maps/search/3100+Market+Street+%0D%0APhiladelphia,+PA+19104?entry=gmail&source=g>
> drexel.edu
>
> --------------------------------------------
>
>
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>

Re: [Xrayutilities-users] XRD-Simulation needs elastic parameters

[Dominik K. <dom...@gm...>]

Dear Rajesh,

Just as an extra warning. Just that the code works for your orthorhombic
system on top of the cubic does not mean it does the correct thing. It
should also be rather clear that the code can not know how the two
materials are stacked on top of each other. (In your case you likely have
some 45degree rotation between the substrate and layer.) So it can only
work if you match it manually. I would be curious what the code does in
your case. can you still share the code you used to build the stack? Maybe
I will add some extra warning when the code is very likely to misbehave.

ad. 1) Regarding the diffraction models: In fact only the kinematical
multibeam and the dynamical model (only full dynamic) are recommended to
use. The substrate can only be really correct with the dynamical model. But
something is wrong with your measurement of the substrate anyways. The
other models are there only for testing the theory I would say. And it's
true that the dynamic one can always only calculate one peak. Since version
1.7.8 you can actually specify a list of hkl, but this list is interpreted
in a way to allow for different hkl values of the film and the substrate.
If you need to simulate multiple peaks of film and substrate you have to
write a small wrapper to do that.

ad 2) I am afraid the relaxation parameter might not be well defined in
your case. this parameter works for cubic on cubic, but likely not for
anything else. At least I never tested it! In your case you will have to
input inplane stress into the stack you build. Unless you do a lot of
testing of the PseudomorphicStack I would recommend to use a LayerStack and
apply the stress/strain manually with the GetStrain/ApplyStrain method of
the material. In this way you can also check the resulting deformation of
the material before you run the simulation. The problem you then have is
that a direct automatic fitting using built in tools in xrayutilities is
currently not possible. You will maybe need some coding for some automatic
fitting, but judging from your experimental data you anyway will never
numerically be able to fit them since in the experiment no thickness
fringes are visible, there is some extra peak, and the substrate seems also
wrong. I would play a bit with manually adjusting the simulation to your
data and stick to that.

kind regards
Dominik

On Fri, Aug 23, 2024 at 12:34 AM Dutta,Rajesh <rd...@dr...> wrote:

> Dear Dominik,
>
>
>
> Many thanks for the fruitful hints. It is doable somehow even though it is
> orthorhombic system on top of cubic. Luckily, our SrFeO2.5 (5.6, 5.65,
> 15.7A) can be treated as pseudocubic system (rotating 45 deg around
> c-axis). With this setting a,b axes of SrFeO2.5 become like cubic
> SrTiO3(3.905A). However, I had to manually build both the SrTiO3 and
> SrFeO2.5 to match the c-axis and to incorporate elastic constants as well.
> Please have a look at the attached figure (simulation and experimental
> data). Let me know your thoughts.
>
>
>
> Besides that, I have questions: (1) Only multibeam kinematical model takes
> all the reflections using “surface_hkl=(0,0,1)” where others take only one
> given (H, K, L). Is there any way to make a list for (H,K,L) so that other
> model can calculate the XRD for several (H,K,L). I tried to give a list but
> did not work. (2) Is the relaxation parameter treated as strain/stress
> here? If not, how can I input in-plane stress or strain? I will try to fit
> the data and let you know the outcomes.
>
>
>
> Thanks again,
>
> Bye,
>
> Rajesh
>
>
>
> *From:* Dominik Kriegner <dom...@gm...>
> *Sent:* Thursday, August 22, 2024 5:46 AM
> *To:* Dutta,Rajesh <rd...@dr...>
> *Cc:* xra...@li...
> *Subject:* Re: [Xrayutilities-users] XRD-Simulation needs elastic
> parameters
>
>
>
> *External.*
>
> Dear Rajesh,
>
>
>
> Is there a standardized way the elastic parameters are provided in the cif
> files? If so one could update the parser to allow to read it properly.
>
>
>
> But likely it's better you define the materials manually. I recommend you
> to look at
>
> https://xrayutilities
> .sourceforge.io/examples.html#using-the-materials-subpackage
>
> I am however afraid I did not include some documentation on how to add the
> elastic parameters. For this maybe best look at how it is done for the
> predefined materials in the code
>
> https://github.com/dkriegner/xrayutilities/blob/main/lib/xrayutilities
> /materials/predefined_materials.py
>
>
>
> Finally I must warn you that I do believe that the pseudomorphic stack was
> never tested for orthorhombic materials on top of a cubic material. I am
> almost certain it won't exactly do what you expect.
>
> You might be able to help yourself and distort the material as you see
> fit, but I would not rely on the pseudomorphicstack code to work without
> changes!
>
>
>
> cheers
>
> Dominik
>
>
>
> On Thu, Aug 22, 2024 at 2:21 AM Dutta, Rajesh via xrayutilities-users <
> xra...@li...> wrote:
>
> Dear xrayutilities users,
>
>
>
> I am very new to this tool. I am trying to build a layer stack of Sr2Fe2O5
> (ortho) on top of SrTiO3 substrate (cubic). I managed to construct the
> model using cif files. However, in the cif file seemingly it is not
> possible to incorporate cij (elastic parameters). Therefore, the fitting
> XRD gives an error saying “layer’ argument needs elastic parameters.
>
>
>
> How to solve this issue while importing cif files. I attach few parts of
> the code below:
>
>
>
> # global parameters
>
> wavelength = xu.wavelength('CuKa1')
>
> offset = -0.00  # angular offset of the zero position of the data
>
>
>
> # set up LayerStack for simulation: SrTiO3/SrFeO2.5
>
> Sr = xu.materials.elements.Sr <http://xu.materials.elements.sr/>
>
> Ti = xu.materials.elements.Ti
>
> O = xu.materials.elements.O
>
> Fe = xu.materials.elements.Fe
>
> STO = xu.materials.Crystal.fromCIF(os.path.join("data", "STO.cif"))
>
> SFO = xu.materials.Crystal.fromCIF(os.path.join("data",
> "Sr2Fe2O5-along.cif"))
>
>
>
> lSTO = xu.simpack.Layer(STO, inf)
>
> lSFO = xu.simpack.Layer(SFO, 800, relaxation=0)
>
>
>
> pstack = xu.simpack.PseudomorphicStack001('list', lSTO, lSFO)
>
>
>
> # set up simulation object
>
> thetaMono = arcsin(wavelength/(2 * xu.materials.Ge.planeDistance(2, 2, 0)))
>
> Cmono = cos(2 * thetaMono)
>
> dyn = xu.simpack.DynamicalModel(pstack, I0=1.5e5, background=0,
>
>                                 resolution_width=2e-3, polarization='both',
>
>                                 Cmono=Cmono)
>
> fitmdyn = xu.simpack.FitModel(dyn)
>
> fitmdyn.set_param_hint('SFO_a', vary=True, min=15.7, max=15.8)
>
> fitmdyn.set_param_hint('STO_a', vary=True, min=3.90, max=3.91)
>
> fitmdyn.set_param_hint('resolution_width', vary=True)
>
> params = fitmdyn.make_params()
>
>
>
> I tried to build the materials using Crystal class and SGLattice, there I
> can define elastic tensors but it does not account proper Wyckoff
> positions, this is why I used cif files.
>
>
>
> Any help, please let me know if you need more info.
>
>
>
> Thanks,
>
> Rajesh
>
>
>
> *-------------------------------------*
>
> *Dr. Rajesh Dutta*
>
>
> *Research Staff Scientist Drexel University College of Engineering
> Pronouns: he/his/him*
>
> Drexel University
> 3100 Market Street
> Philadelphia, PA 19104
> drexel.edu
>
> --------------------------------------------
>
>
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>
>

Re: [Xrayutilities-users] XRD-Simulation needs elastic parameters

[Dutta,Rajesh <rd...@dr...>]

Dear Dominik,

Many thanks for the fruitful hints. It is doable somehow even though it is orthorhombic system on top of cubic. Luckily, our SrFeO2.5 (5.6, 5.65, 15.7A) can be treated as pseudocubic system (rotating 45 deg around c-axis). With this setting a,b axes of SrFeO2.5 become like cubic SrTiO3(3.905A). However, I had to manually build both the SrTiO3 and SrFeO2.5 to match the c-axis and to incorporate elastic constants as well. Please have a look at the attached figure (simulation and experimental data). Let me know your thoughts.

Besides that, I have questions: (1) Only multibeam kinematical model takes all the reflections using “surface_hkl=(0,0,1)” where others take only one given (H, K, L). Is there any way to make a list for (H,K,L) so that other model can calculate the XRD for several (H,K,L). I tried to give a list but did not work. (2) Is the relaxation parameter treated as strain/stress here? If not, how can I input in-plane stress or strain? I will try to fit the data and let you know the outcomes.

Thanks again,
Bye,
Rajesh

From: Dominik Kriegner <dom...@gm...>
Sent: Thursday, August 22, 2024 5:46 AM
To: Dutta,Rajesh <rd...@dr...>
Cc: xra...@li...
Subject: Re: [Xrayutilities-users] XRD-Simulation needs elastic parameters


External.
Dear Rajesh,

Is there a standardized way the elastic parameters are provided in the cif files? If so one could update the parser to allow to read it properly.

But likely it's better you define the materials manually. I recommend you to look at
https://xrayutilities.sourceforge.io/examples.html#using-the-materials-subpackage
I am however afraid I did not include some documentation on how to add the elastic parameters. For this maybe best look at how it is done for the predefined materials in the code
https://github.com/dkriegner/xrayutilities/blob/main/lib/xrayutilities/materials/predefined_materials.py

Finally I must warn you that I do believe that the pseudomorphic stack was never tested for orthorhombic materials on top of a cubic material. I am almost certain it won't exactly do what you expect.
You might be able to help yourself and distort the material as you see fit, but I would not rely on the pseudomorphicstack code to work without changes!

cheers
Dominik

On Thu, Aug 22, 2024 at 2:21 AM Dutta, Rajesh via xrayutilities-users <xra...@li...<mailto:xra...@li...>> wrote:
Dear xrayutilities users,

I am very new to this tool. I am trying to build a layer stack of Sr2Fe2O5 (ortho) on top of SrTiO3 substrate (cubic). I managed to construct the model using cif files. However, in the cif file seemingly it is not possible to incorporate cij (elastic parameters). Therefore, the fitting XRD gives an error saying “layer’ argument needs elastic parameters.

How to solve this issue while importing cif files. I attach few parts of the code below:

# global parameters
wavelength = xu.wavelength('CuKa1')
offset = -0.00  # angular offset of the zero position of the data

# set up LayerStack for simulation: SrTiO3/SrFeO2.5
Sr = xu.materials.elements.Sr<http://xu.materials.elements.sr/>
Ti = xu.materials.elements.Ti
O = xu.materials.elements.O
Fe = xu.materials.elements.Fe
STO = xu.materials.Crystal.fromCIF(os.path.join("data", "STO.cif"))
SFO = xu.materials.Crystal.fromCIF(os.path.join("data", "Sr2Fe2O5-along.cif"))

lSTO = xu.simpack.Layer(STO, inf)
lSFO = xu.simpack.Layer(SFO, 800, relaxation=0)

pstack = xu.simpack.PseudomorphicStack001('list', lSTO, lSFO)

# set up simulation object
thetaMono = arcsin(wavelength/(2 * xu.materials.Ge.planeDistance(2, 2, 0)))
Cmono = cos(2 * thetaMono)
dyn = xu.simpack.DynamicalModel(pstack, I0=1.5e5, background=0,
                                resolution_width=2e-3, polarization='both',
                                Cmono=Cmono)
fitmdyn = xu.simpack.FitModel(dyn)
fitmdyn.set_param_hint('SFO_a', vary=True, min=15.7, max=15.8)
fitmdyn.set_param_hint('STO_a', vary=True, min=3.90, max=3.91)
fitmdyn.set_param_hint('resolution_width', vary=True)
params = fitmdyn.make_params()

I tried to build the materials using Crystal class and SGLattice, there I can define elastic tensors but it does not account proper Wyckoff positions, this is why I used cif files.

Any help, please let me know if you need more info.

Thanks,
Rajesh

-------------------------------------
Dr. Rajesh Dutta
Research Staff Scientist
Drexel University College of Engineering
Pronouns: he/his/him

Drexel University
3100 Market Street
Philadelphia, PA 19104
drexel.edu<http://drexel.edu/>
--------------------------------------------

_______________________________________________
xrayutilities-users mailing list
xra...@li...<mailto:xra...@li...>
https://lists.sourceforge.net/lists/listinfo/xrayutilities-users

Re: [Xrayutilities-users] XRD-Simulation needs elastic parameters

[Dominik K. <dom...@gm...>]

Dear Rajesh,

Is there a standardized way the elastic parameters are provided in the cif
files? If so one could update the parser to allow to read it properly.

But likely it's better you define the materials manually. I recommend you
to look at
https://xrayutilities
.sourceforge.io/examples.html#using-the-materials-subpackage
I am however afraid I did not include some documentation on how to add the
elastic parameters. For this maybe best look at how it is done for the
predefined materials in the code
https://github.com/dkriegner/xrayutilities/blob/main/lib/xrayutilities
/materials/predefined_materials.py

Finally I must warn you that I do believe that the pseudomorphic stack was
never tested for orthorhombic materials on top of a cubic material. I am
almost certain it won't exactly do what you expect.
You might be able to help yourself and distort the material as you see fit,
but I would not rely on the pseudomorphicstack code to work without changes!

cheers
Dominik

On Thu, Aug 22, 2024 at 2:21 AM Dutta, Rajesh via xrayutilities-users <
xra...@li...> wrote:

> Dear xrayutilities users,
>
>
>
> I am very new to this tool. I am trying to build a layer stack of Sr2Fe2O5
> (ortho) on top of SrTiO3 substrate (cubic). I managed to construct the
> model using cif files. However, in the cif file seemingly it is not
> possible to incorporate cij (elastic parameters). Therefore, the fitting
> XRD gives an error saying “layer’ argument needs elastic parameters.
>
>
>
> How to solve this issue while importing cif files. I attach few parts of
> the code below:
>
>
>
> # global parameters
>
> wavelength = xu.wavelength('CuKa1')
>
> offset = -0.00  # angular offset of the zero position of the data
>
>
>
> # set up LayerStack for simulation: SrTiO3/SrFeO2.5
>
> Sr = xu.materials.elements.Sr
>
> Ti = xu.materials.elements.Ti
>
> O = xu.materials.elements.O
>
> Fe = xu.materials.elements.Fe
>
> STO = xu.materials.Crystal.fromCIF(os.path.join("data", "STO.cif"))
>
> SFO = xu.materials.Crystal.fromCIF(os.path.join("data",
> "Sr2Fe2O5-along.cif"))
>
>
>
> lSTO = xu.simpack.Layer(STO, inf)
>
> lSFO = xu.simpack.Layer(SFO, 800, relaxation=0)
>
>
>
> pstack = xu.simpack.PseudomorphicStack001('list', lSTO, lSFO)
>
>
>
> # set up simulation object
>
> thetaMono = arcsin(wavelength/(2 * xu.materials.Ge.planeDistance(2, 2, 0)))
>
> Cmono = cos(2 * thetaMono)
>
> dyn = xu.simpack.DynamicalModel(pstack, I0=1.5e5, background=0,
>
>                                 resolution_width=2e-3, polarization='both',
>
>                                 Cmono=Cmono)
>
> fitmdyn = xu.simpack.FitModel(dyn)
>
> fitmdyn.set_param_hint('SFO_a', vary=True, min=15.7, max=15.8)
>
> fitmdyn.set_param_hint('STO_a', vary=True, min=3.90, max=3.91)
>
> fitmdyn.set_param_hint('resolution_width', vary=True)
>
> params = fitmdyn.make_params()
>
>
>
> I tried to build the materials using Crystal class and SGLattice, there I
> can define elastic tensors but it does not account proper Wyckoff
> positions, this is why I used cif files.
>
>
>
> Any help, please let me know if you need more info.
>
>
>
> Thanks,
>
> Rajesh
>
>
>
> *-------------------------------------*
>
> *Dr. Rajesh Dutta*
>
>
> *Research Staff Scientist Drexel University College of Engineering
> Pronouns: he/his/him*
>
> Drexel University
> 3100 Market Street
> Philadelphia, PA 19104
> drexel.edu
>
> --------------------------------------------
>
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>

[Xrayutilities-users] XRD-Simulation needs elastic parameters

[Dutta,Rajesh <rd...@dr...>]

Dear xrayutilities users,

I am very new to this tool. I am trying to build a layer stack of Sr2Fe2O5 (ortho) on top of SrTiO3 substrate (cubic). I managed to construct the model using cif files. However, in the cif file seemingly it is not possible to incorporate cij (elastic parameters). Therefore, the fitting XRD gives an error saying "layer' argument needs elastic parameters.

How to solve this issue while importing cif files. I attach few parts of the code below:

# global parameters
wavelength = xu.wavelength('CuKa1')
offset = -0.00  # angular offset of the zero position of the data

# set up LayerStack for simulation: SrTiO3/SrFeO2.5
Sr = xu.materials.elements.Sr
Ti = xu.materials.elements.Ti
O = xu.materials.elements.O
Fe = xu.materials.elements.Fe
STO = xu.materials.Crystal.fromCIF(os.path.join("data", "STO.cif"))
SFO = xu.materials.Crystal.fromCIF(os.path.join("data", "Sr2Fe2O5-along.cif"))

lSTO = xu.simpack.Layer(STO, inf)
lSFO = xu.simpack.Layer(SFO, 800, relaxation=0)

pstack = xu.simpack.PseudomorphicStack001('list', lSTO, lSFO)

# set up simulation object
thetaMono = arcsin(wavelength/(2 * xu.materials.Ge.planeDistance(2, 2, 0)))
Cmono = cos(2 * thetaMono)
dyn = xu.simpack.DynamicalModel(pstack, I0=1.5e5, background=0,
                                resolution_width=2e-3, polarization='both',
                                Cmono=Cmono)
fitmdyn = xu.simpack.FitModel(dyn)
fitmdyn.set_param_hint('SFO_a', vary=True, min=15.7, max=15.8)
fitmdyn.set_param_hint('STO_a', vary=True, min=3.90, max=3.91)
fitmdyn.set_param_hint('resolution_width', vary=True)
params = fitmdyn.make_params()

I tried to build the materials using Crystal class and SGLattice, there I can define elastic tensors but it does not account proper Wyckoff positions, this is why I used cif files.

Any help, please let me know if you need more info.

Thanks,
Rajesh

-------------------------------------
Dr. Rajesh Dutta
Research Staff Scientist
Drexel University College of Engineering
Pronouns: he/his/him

Drexel University
3100 Market Street
Philadelphia, PA 19104
drexel.edu<http://drexel.edu/>
--------------------------------------------

Re: [Xrayutilities-users] Need some guidance for HRXRD twotheta-omega and omega-twotheta scans

[Dominik K. <dom...@gm...>]

Dear Allen,

few hints for your questions:

If you will need InGaP often and all the variation of the lattice parameter
and other needed parameters (elasticity?) are known well enough, then I
think it would make sense to create a class derived from the 'Alloy' or
'CubicAlloy' classes like SiGe and AlGaAs.

Regarding the scan directions on top of the reciprocal space maps: have a
look here:
https://xrayutilities.sourceforge.io/examples.html#line-cuts-from-reciprocal-space-maps
and in the example
https://github.com/dkriegner/xrayutilities/blob/main/examples/xrayutilities_read_panalytical.py
There such scan directions are shown on top of reciprocal space maps. These
directions can be automatically generated by doing line cuts.

cheers
Dominik

On Fri, Mar 3, 2023 at 5:56 AM Allen Hall <aj...@gm...> wrote:

> Hi Dominik!
>
> Thanks so much for this discussion/information regarding the package!
> This is great news!  Yes, I had a feeling it was 2theta-omega, but wasn't
> sure on this... and you are of course correct it really only makes sense
> for epitaxial crystals to use radial scans (with the exception of the
> omega-rocking curve).  Coming from the machine side, I'm used to using the
> machines only in angle space, not in Qspace - so it takes a bit of head
> scratching here and there to mentally go back and forth... I'm still
> learning from your examples here.
>
> A few q's... I need to make an InGaP for my current work, and I see the
> example for InP in the docs.  I have in the past imported CIF's for say
> CuInSe2, and that worked out ok... but wasn't sure if I should ask about
> making a class like AlGaAs... there are a number of mixtures that are
> similar to the AlGaAs issue - are these difficult to create?  I could stick
> to a common star-file ICDD file example of InGaP, but I wasn't sure if that
> was limiting for modelling purposes.  [I'm hoping to start simple here so
> probably thinking about a new class is a bad idea to start with.]
>
> Lastly- an idea that might be cute... I'm tempted to try and draw lines
> ontop of the RSM diffraction spot presentation... one could probably show
> what a 2-theta-omega or omega or theta scan looked like at specific angles
> but represented in q-space as a line or even curved square for planar
> detectors... would this be farily easy to plot directly onto the same
> axes?  I guess we'd have to generate the poins in q-space based on the scan
> parameters and then add them to the plot...
>
> Thanks so much for the excellent package!  I'm enjoying learning from the
> examples and the mailing list here.  Big cheers,
> -Allen
>
>
> Allen Hall
> aj...@gm...
> al...@al...
> (old:ah...@il...)
>
>
> On Sat, Feb 25, 2023 at 10:50 AM Dominik Kriegner <
> dom...@gm...> wrote:
>
>> Dear Allen,
>>
>> the simpack_xrd_InAs_fitting of course models a radial 2theta-omega scan.
>> The documentation examples (
>> https://xrayutilities.sourceforge.io/simulations.html) also clearly
>> specify that all models are for crystal truncation rod analysis (and are
>> mostly tested for the symmetric 2theta-omega case). A pure 2theta scan
>> would make not so much sense for an epitaxial system. so pure 2Theta scans
>> can actually (somewhat limited) in xrayutilities only be simulated for
>> powder/textured samples.
>>
>> So actually all "XRD" simulation examples are basically what you look
>> for. I think the example file simpack_xrd_SiGe_superlattice.py could be
>> particularly interesting since it shows also how a slightly more complex
>> layer structure can be built.
>>
>> hope this helps
>> Dominik
>>
>

Re: [Xrayutilities-users] Need some guidance for HRXRD twotheta-omega and omega-twotheta scans

[Allen H. <aj...@gm...>]

Hi Dominik!

Thanks so much for this discussion/information regarding the package!  This
is great news!  Yes, I had a feeling it was 2theta-omega, but wasn't sure
on this... and you are of course correct it really only makes sense for
epitaxial crystals to use radial scans (with the exception of the
omega-rocking curve).  Coming from the machine side, I'm used to using the
machines only in angle space, not in Qspace - so it takes a bit of head
scratching here and there to mentally go back and forth... I'm still
learning from your examples here.

A few q's... I need to make an InGaP for my current work, and I see the
example for InP in the docs.  I have in the past imported CIF's for say
CuInSe2, and that worked out ok... but wasn't sure if I should ask about
making a class like AlGaAs... there are a number of mixtures that are
similar to the AlGaAs issue - are these difficult to create?  I could stick
to a common star-file ICDD file example of InGaP, but I wasn't sure if that
was limiting for modelling purposes.  [I'm hoping to start simple here so
probably thinking about a new class is a bad idea to start with.]

Lastly- an idea that might be cute... I'm tempted to try and draw lines
ontop of the RSM diffraction spot presentation... one could probably show
what a 2-theta-omega or omega or theta scan looked like at specific angles
but represented in q-space as a line or even curved square for planar
detectors... would this be farily easy to plot directly onto the same
axes?  I guess we'd have to generate the poins in q-space based on the scan
parameters and then add them to the plot...

Thanks so much for the excellent package!  I'm enjoying learning from the
examples and the mailing list here.  Big cheers,
-Allen


Allen Hall
aj...@gm...
al...@al...
(old:ah...@il...)


On Sat, Feb 25, 2023 at 10:50 AM Dominik Kriegner <
dom...@gm...> wrote:

> Dear Allen,
>
> the simpack_xrd_InAs_fitting of course models a radial 2theta-omega scan.
> The documentation examples (
> https://xrayutilities.sourceforge.io/simulations.html) also clearly
> specify that all models are for crystal truncation rod analysis (and are
> mostly tested for the symmetric 2theta-omega case). A pure 2theta scan
> would make not so much sense for an epitaxial system. so pure 2Theta scans
> can actually (somewhat limited) in xrayutilities only be simulated for
> powder/textured samples.
>
> So actually all "XRD" simulation examples are basically what you look for.
> I think the example file simpack_xrd_SiGe_superlattice.py could be
> particularly interesting since it shows also how a slightly more complex
> layer structure can be built.
>
> hope this helps
> Dominik
>

Re: [Xrayutilities-users] Need some guidance for HRXRD twotheta-omega and omega-twotheta scans

[Dominik K. <dom...@gm...>]

Dear Allen,

the simpack_xrd_InAs_fitting of course models a radial 2theta-omega scan.
The documentation examples (
https://xrayutilities.sourceforge.io/simulations.html) also clearly specify
that all models are for crystal truncation rod analysis (and are mostly
tested for the symmetric 2theta-omega case). A pure 2theta scan would make
not so much sense for an epitaxial system. so pure 2Theta scans can
actually (somewhat limited) in xrayutilities only be simulated for
powder/textured samples.

So actually all "XRD" simulation examples are basically what you look for.
I think the example file simpack_xrd_SiGe_superlattice.py could be
particularly interesting since it shows also how a slightly more complex
layer structure can be built.

hope this helps
Dominik

[Xrayutilities-users] Need some guidance for HRXRD twotheta-omega and omega-twotheta scans

[Allen H. <aj...@gm...>]

Hi Xrayutilities users!

I'm back again it seems... doing more in python these days, and revisited
xrayutilities to do some simulations and viewing reciprocal space for
different substrates.

I need to work on some omega-twotheta and two-theta-omega scans... it seems
that doing q-space work is fairly straight forward based on the examples,
but I don't see any great examples for the simple 0D detector doing
two-theta-omega scans?  There's one example of fitting to a two-theta scan
(is it purely two-theta or is it two-theta-omega?) with a RASfile
(unfortunately I can't see the Rasfile internals in the variable browser,
so will read about the structure of the RAS importer... )  I have parsed
imported data that was unstructured data from a fairly old system that I'd
like to simulate and also attempt fitting, so this example appears the
closest to me for the analysis.

Is the two-theta scan in the example "simpack_xrd_InAs_fitting.py" actually
a two-theta-omega scan?  Is the resulting graph any different in simulation
if we only give it two-theta -v- two-theta omega? (seems it would be a
different scan in q-space for asymmetric peaks? maybe not for symmetric
peaks...)

Would love to see a simple simulation in two-theta-omega or omega-two-theta
space with multilayers.

Any and all pointers are greatly appreciated!  I'll be attempting to apply
this to fairly complicated layer stacks if this works out.

Thanks so much!
-Allen


Allen Hall
aj...@gm...
al...@al...
(old:ah...@il...)

Re: [Xrayutilities-users] Disable warning while Gridding

[Dominik K. <dom...@gm...>]

Hi Carsten,

Unfortunately, currently warnings coming from the C-code (like the one 
you mention) can't be influenced.

Generally warnings (printouts from the Python code) should all be 
removed when setting a lower `xrayutilities.config.VERBOSITY` (e.g. 0).

I will fix/change the c-code to also respect this verbosity setting and 
remove this (and maybe other warnings) if `VERBOSITY` is set to zero.

I have created a GitHub issue so that everyone can see when this change 
is implemented:
https://github.com/dkriegner/xrayutilities/issues/145

cheers
Dominik

On 11/01/2023 11.23, Richter, Dr. Carsten wrote:
> 
> Dear all,
> 
> when using the gridders, it may happen that some data points are outside 
> a range that is fixed which causes this warning:
> 
> “XU.Gridder3D(c): more than half of the datapoints out of the data 
> range, consider regridding with extended range!”
> 
> Is it possible to disable the warning? This is a bit annoying when 
> gridding a large amount of data in serial manner (the warning repeats 
> during each call of the ridder).
> 
> Thanks
> 
> Carsten
> 
> =================================
> 
> Leibniz-Institut für Kristallzüchtung (IKZ)
> 
> https://www.ikz-berlin.de
> 
> Max Born Str. 2
> 
> 12489 Berlin / Germany
> 
> Phone: +49 30 6392 2859
> 
> 
> ------------------------------------------------------------------------
> Dr. Carsten Richter
> NachwuchsgruppenleiterX-Ray Imaging
> Materialwissenschaften/Experimentelle Charakterisierung
> T: +49 (0)30 6392 2859
> F: +49 (0)30 6392 3003
> E: car...@ik... <mailto:car...@ik...>
> 
> 	
> LEIBNIZ-INSTITUT
> FÜR KRISTALLZÜCHTUNG
> im Forschungsverbund Berlin e.V
> Max-Born-Straße 2
> 12489 Berlin
> www.ikz-berlin.de <https://www.ikz-berlin.de/>
> 
> ------------------------------------------------------------------------
> 
> Diese Nachricht enthält vertrauliche Informationen und ist nur für die 
> genannten Empfänger bestimmt. Falls Sie kein genannter Empfänger sind, 
> dürfen Sie diese E-Mail nicht verbreiten, verteilen oder kopieren. Bitte 
> benachrichtigen Sie car...@ik... umgehend per E-Mail, 
> falls Sie diese E-Mail fälschlicherweise erhalten haben, und löschen Sie 
> sie von lhrem System. Eine sichere und fehlerfreie E-Mail-Übertragung 
> kann nicht gewährleistet werden, da Informationen abgefangen, 
> beschädigt, zerstört, verzögert werden, verloren gehen, unvollständig 
> sein oder Viren enthalten können. Aus diesem Grund übernimmt  keine 
> Haftung für jedwede Fehler oder Auslassungen in dieser Nachricht, die 
> auf eine E-Mail-Übertragung zurückzuführen sind. Falls eine Bestätigung 
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> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users

[Xrayutilities-users] Disable warning while Gridding

[Richter, D. C. <car...@ik...>]

Dear all,

when using the gridders, it may happen that some data points are outside a range that is fixed which causes this warning:

“XU.Gridder3D(c): more than half of the datapoints out of the data range, consider regridding with extended range!”

Is it possible to disable the warning? This is a bit annoying when gridding a large amount of data in serial manner (the warning repeats during each call of the ridder).

Thanks
Carsten

=================================

Leibniz-Institut für Kristallzüchtung (IKZ)
https://www.ikz-berlin.de
Max Born Str. 2
12489 Berlin / Germany

Phone: +49 30 6392 2859


________________________________
Dr. Carsten Richter
Nachwuchsgruppenleiter X-Ray Imaging
Materialwissenschaften/Experimentelle Charakterisierung
T: +49 (0)30 6392 2859
F: +49 (0)30 6392 3003
E: car...@ik...<mailto:car...@ik...>


[cid:image3836ad.PNG@4b6d40c0.4b8eb113]
LEIBNIZ-INSTITUT
FÜR KRISTALLZÜCHTUNG
im Forschungsverbund Berlin e.V

Max-Born-Straße 2
12489 Berlin
www.ikz-berlin.de<https://www.ikz-berlin.de/>

________________________________

Diese Nachricht enthält vertrauliche Informationen und ist nur für die genannten Empfänger bestimmt. Falls Sie kein genannter Empfänger sind, dürfen Sie diese E-Mail nicht verbreiten, verteilen oder kopieren. Bitte benachrichtigen Sie car...@ik... umgehend per E-Mail, falls Sie diese E-Mail fälschlicherweise erhalten haben, und löschen Sie sie von lhrem System. Eine sichere und fehlerfreie E-Mail-Übertragung kann nicht gewährleistet werden, da Informationen abgefangen, beschädigt, zerstört, verzögert werden, verloren gehen, unvollständig sein oder Viren enthalten können. Aus diesem Grund übernimmt  keine Haftung für jedwede Fehler oder Auslassungen in dieser Nachricht, die auf eine E-Mail-Übertragung zurückzuführen sind. Falls eine Bestätigung erforderlich ist, fordern Sie bitte eine gedruckte Version an.

Re: [Xrayutilities-users] Single Crystal Diffraction Simulation

[Dominik K. <dom...@gm...>]

Dear Mischa,

If you are already adapting the code and are comfortable with that then 
I think you should be able to achieve what you are looking for.

The example you mention should be a good starting point.

Now to change the crystal alignment I think there are two main options:

1) If you turn the crystal using a goniometer then it should be straight 
forward to obtain the rotation matrix the goniometer rotations 
correspond to and apply this transformation to the Bragg peak positions.

2) In the example you mention [1] there are used two crystal directions 
which define the orientation of the crystal in the experiment. e.g. line 
9 of the code uses 11-2 and 111 directions to orient the substrate. You 
can change/turn those two vectors and therefore also effectively change 
the orientation. Just be sure to keep using two perpendicular 
directions. The HXRD initialization otherwise will use some projections 
(and should print out a warning/message).

I hope this helps. Also if you manage to obtain something useful it 
would be nice to contribute the resulting function/script via a Github 
Pull request.

cheers
Dominik

[1] 
https://xrayutilities.sourceforge.io/examples.html#visualization-of-the-bragg-peaks-in-a-reciprocal-space-plane

On 04/01/2023 11.47, Mischa Stifter wrote:
> Dear Xrayutilities-Team,
> 
> I am currently looking for a single crystal diffraction simulator. Your 
> package seems very promising for that since it’s very strong and 
> provides all degrees of changeability in an experimental setup. 
> Unfortunately, I didn’t figure it out yet, how to use it in the proper 
> manner.
> 
> What I am looking for is, a changeable crystal alignment in an X-ray 
> beam that produces a single diffraction pattern on the detector for 
> further use. (I have currently worked with the Laue method and am 
> therefore thinking in that kind of setups etc.) I was able to modify the 
> example of section ‘Visualization of the Bragg peaks in a reciprocal 
> space plane’ to a full image, because that seems for me as the starting 
> point. But now I am stuck on how to rotate the crystal in the 
> experimental alignment. Best would be to have just the crystal 
> orientation as a free parameter, without the detector aswell.
> 
> Is there this possibility of creating such patterns and if yes can you 
> help me to get it done?
> 
> Thanks a lot for your help!
> Best,
> 
> Mischa
> 
> 
> 
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users