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From: Dominik K. <dom...@gm...> - 2025-02-19 06:15:04
|
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. > |
|
From: Kusch, M. <max...@he...> - 2025-02-18 08:49:30
|
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. |
|
From: Dominik K. <dom...@gm...> - 2025-02-17 20:48:30
|
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 > |
|
From: Kusch, M. <max...@he...> - 2025-02-17 14:11:42
|
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. |
|
From: Dominik K. <dom...@gm...> - 2024-09-30 07:30:30
|
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 > |
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From: Richter, D. C. <car...@ik...> - 2024-09-25 09:30:17
|
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. |
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From: Dominik K. <dom...@gm...> - 2024-08-24 05:45:18
|
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 > |
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From: Dutta,Rajesh <rd...@dr...> - 2024-08-23 21:11:55
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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 |
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From: Paritosh W. <par...@gm...> - 2024-08-23 09:51:19
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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 > |
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From: Dominik K. <dom...@gm...> - 2024-08-23 08:54:25
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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 > > |
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From: Dutta,Rajesh <rd...@dr...> - 2024-08-23 01:10:41
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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 |
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From: Dominik K. <dom...@gm...> - 2024-08-22 09:46:39
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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 > |
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From: Dutta,Rajesh <rd...@dr...> - 2024-08-22 00:21:23
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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/>
--------------------------------------------
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From: Dominik K. <dom...@gm...> - 2023-03-03 07:42:53
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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 >> > |
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From: Allen H. <aj...@gm...> - 2023-03-03 04:56:45
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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 > |
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From: Dominik K. <dom...@gm...> - 2023-02-25 16:50:15
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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 |
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From: Allen H. <aj...@gm...> - 2023-02-24 21:23:06
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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...) |
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From: Dominik K. <dom...@gm...> - 2023-01-11 12:00:39
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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 > erforderlich ist, fordern Sie bitte eine gedruckte Version an. > > > > > _______________________________________________ > xrayutilities-users mailing list > xra...@li... > https://lists.sourceforge.net/lists/listinfo/xrayutilities-users |
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From: Richter, D. C. <car...@ik...> - 2023-01-11 10:40:21
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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. |
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From: Dominik K. <dom...@gm...> - 2023-01-04 13:06:51
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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 |
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From: Mischa S. <mis...@uz...> - 2023-01-04 11:02:46
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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 |
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From: Dominik K. <dom...@gm...> - 2022-10-31 13:33:21
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xrayutilities-1.7.4 is available This version is compatible with Python >3.6. Version 1.7.4 contains several bug fixes. In particular it contains [1]: * fix for a mistake in the docstring of the March-Dollase texture model in xu.simpack.Powder, * a correction of the Poisson ratio of the GaInAs Darwin model, * new GetStrain and GeStress functions for xu.material.Material (Github Pull request #138) * improvements for kappa goniometers and removal of some deprecated scipy namespaces. In order to obtain the new version, go to SourceForge [2] or use PyPI [3]. Wheel packages for Windows, macOS and Linux are found on PyPI for 64-bit Python in versions 3.6, 3.7, 3.8, 3.9, and 3.10. There is also a conda-forge package [4]. If you encounter problems, please report them on GitHub or on the mailinglist [5]. [1] https://github.com/dkriegner/xrayutilities/blob/main/CHANGES.txt [2] https://sourceforge.net/projects/xrayutilities [3] https://pypi.python.org/pypi/xrayutilities [4] https://github.com/conda-forge/xrayutilities-feedstock [5] https://sourceforge.net/p/xrayutilities/mailman/xrayutilities-users/ |
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From: Dominik K. <dom...@gm...> - 2021-12-13 20:59:44
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Hi Allen, let me comment on your remaining questions below On Mon, Dec 13, 2021 at 4:53 PM Allen Hall <aj...@gm...> wrote: > One thing I don't see is a description of the resulting vector from > clicking the plot (for example): > GaAs > hkl: (1, 3, -1) > angles: [-31.6513 0. 0. 53.7331] > > It appears that this is [ om, ?, ?, ttheta] > > Are the others Psi or Chi and Phi? > yes those other two are the sample tilt and sample azimuth. I have changed the print statement to include the angle names. > > Is there a method to rotate all spots from all rotations in Phi into the > RSM? (this would look weird, so I would suspect not- we'd get streaks > on the RSM I believe). > Actually there is a possibility show all peaks by projecting them into the plot plane. There are two options for that which can be controlled by the 'projection' and 'maxqout' arguments to show_reciprocal_space_plane see: https://xrayutilities.sourceforge.io/xrayutilities.materials.html?highlight=show_reciprocal#xrayutilities.materials.plot.show_reciprocal_space_plane > > Also- is the red halo around the plot the ttmax = 160 (for example). > yes , the red area is the one you can only access by angles above ttmax. > I don't notice a change when I request a Laue zone plot... > This is because its by default on. The option is only there to switch it off in case one does not want it. cheers dominik > > Thanks so much for this utility and the ability to ask questions on the > mailing list here! I really appreciate it! > -Allen > > -- > Allen Hall > aj...@gm... > al...@il... > > |
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From: Allen H. <aj...@gm...> - 2021-12-13 15:53:50
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Hi Dominik! Thanks for the warm welcome! Yes, I see now that the GaAs .cif was imported to my local database. I hope that the chemical info isn't very critical for S calculations. And you're absolutely right, I needed to specify an in-plane primary beam direction in the plot, it seems I've gone and mixed up a few errors here. My apologies! And thank you for explaining. One thing I don't see is a description of the resulting vector from clicking the plot (for example): GaAs hkl: (1, 3, -1) angles: [-31.6513 0. 0. 53.7331] It appears that this is [ om, ?, ?, ttheta] Are the others Psi or Chi and Phi? Is there a method to rotate all spots from all rotations in Phi into the RSM? (this would look weird, so I would suspect not- we'd get streaks on the RSM I believe). Also- is the red halo around the plot the ttmax = 160 (for example). I don't notice a change when I request a Laue zone plot... Thanks so much for this utility and the ability to ask questions on the mailing list here! I really appreciate it! -Allen -- Allen Hall aj...@gm... al...@il... |
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From: Dominik K. <dom...@gm...> - 2021-12-11 08:24:50
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HI Allen,
welcome to the mailing list.
The problem you experience seems to be unrelated to the CIF file import.
The code you sent works for me by only printing a message (a warning).
GaAs = xu.materials.Crystal.fromCIF("gaas4.cif")
XU.materials: element As used instead of As3-
This warning informs you that for the oxidation state used in the CIF file
no atomic form factors are available and that the neutral atom is used
instead.
Only for selected elements form factor information is available for various
oxidation states. Here xrayutilities just relies on information from common
databases. If there are some available which contain more information it
could be included. The oxidation state does however usually not change much
with respect to X-ray diffraction (only would slightly change the
intensities of peaks).
The error you mention seems to be related to the fact that you forgot to
specify the second obligatory argument to the HXRD class constructor.
HXRD is derived from Experiment which documents the parameters which need
to be used here:
https://xrayutilities.sourceforge.io/xrayutilities.html?highlight=hxrd#xrayutilities.experiment.Experiment.__init__
A full example of HXRD use can be found here:
https://xrayutilities.sourceforge.io/examples.html#angle-calculation-using-experiment-and-materials-classes
or here:
https://github.com/dkriegner/xrayutilities/blob/main/examples/xrayutilities_show_reciprocal_space_plane.py
The latter script directly produces a plot which shows the various Bragg
peaks within one plane of reciprocal space. If you use some interactive
plot backend you can click on a peak and get its diffraction angles.
cheers
Dominik
On Fri, Dec 10, 2021 at 9:49 PM Allen Hall <aj...@gm...> wrote:
> Hi XrayUtilities Mailing list!!
>
> Great python package!!
>
> I'm attempting to use the CIF import to run an RS visualization on a
> substrate (for peak finding purposes), and I'm using the following for
> import:
>
> import os
>
> import numpy
> import xrayutilities as xu
>
> # create material
> GaAs = xu.materials.Crystal.fromCIF(os.path.join("data", "gaas4.cif"))
>
> The error:
> XU.materials: element As used instead of As3-
> Traceback (most recent call last):
>
> File "/Users/allenhall/Desktop/reciprocal
> space/xrayutilities-main/examples/GaAs RSM attempt.py", line 18, in
> <module>
> geom = xu.HXRD(GaAs.Q(1, 1, 1))
>
> TypeError: __init__() missing 1 required positional argument: 'ndir'
>
> To help in completeness, I'm adding the full text of the CIF file I have
> for GaAs here:
>
> data_43359-ICSD
> #©2003 by Fachinformationszentrum Karlsruhe, and the U.S. Secretary of
> #Commerce on behalf of the United States. All rights reserved.
> _database_code_ICSD 43359
> _audit_creation_date 2000/07/15
> _chemical_name_systematic 'Gallium Arsenide'
> _chemical_formula_structural 'Ga As'
> _chemical_formula_sum 'As1 Ga1'
> _publ_section_title
> ;
> An X-ray study of some A(III) B(V) compounds which display deviataion
> from stoichoimetry
> ;
> loop_
> _citation_id
> _citation_journal_abbrev
> _citation_year
> _citation_journal_volume
> _citation_page_first
> _citation_page_last
> _citation_journal_id_ASTM
> primary Kristallografiya 1962 7 850 853 KRISAJ
> loop_
> _publ_author_name
> 'Ozolins, G.'
> 'Averkieva, G.K.'
> 'Ievins, A.'
> 'Goryunova, N.A.'
> _cell_length_a 5.65317(10)
> _cell_length_b 5.65317
> _cell_length_c 5.65317
> _cell_angle_alpha 90.
> _cell_angle_beta 90.
> _cell_angle_gamma 90.
> _cell_volume 180.67
> _cell_formula_units_Z 4
> _symmetry_space_group_name_H-M 'F -4 3 m'
> _symmetry_Int_Tables_number 216
> loop_
> _symmetry_equiv_pos_site_id
> _symmetry_equiv_pos_as_xyz
> 1 '-z, -y, x'
> 2 '-y, -x, z'
> 3 '-x, -z, y'
> 4 '-z, -x, y'
> 5 '-y, -z, x'
> 6 '-x, -y, z'
> 7 '-z, y, -x'
> 8 '-y, x, -z'
> 9 '-x, z, -y'
> 10 '-z, x, -y'
> 11 '-y, z, -x'
> 12 '-x, y, -z'
> 13 'z, -y, -x'
> 14 'y, -x, -z'
> 15 'x, -z, -y'
> 16 'z, -x, -y'
> 17 'y, -z, -x'
> 18 'x, -y, -z'
> 19 'z, y, x'
> 20 'y, x, z'
> 21 'x, z, y'
> 22 'z, x, y'
> 23 'y, z, x'
> 24 'x, y, z'
> 25 '-z, -y+1/2, x+1/2'
> 26 '-z+1/2, -y, x+1/2'
> 27 '-z+1/2, -y+1/2, x'
> 28 '-y, -x+1/2, z+1/2'
> 29 '-y+1/2, -x, z+1/2'
> 30 '-y+1/2, -x+1/2, z'
> 31 '-x, -z+1/2, y+1/2'
> 32 '-x+1/2, -z, y+1/2'
> 33 '-x+1/2, -z+1/2, y'
> 34 '-z, -x+1/2, y+1/2'
> 35 '-z+1/2, -x, y+1/2'
> 36 '-z+1/2, -x+1/2, y'
> 37 '-y, -z+1/2, x+1/2'
> 38 '-y+1/2, -z, x+1/2'
> 39 '-y+1/2, -z+1/2, x'
> 40 '-x, -y+1/2, z+1/2'
> 41 '-x+1/2, -y, z+1/2'
> 42 '-x+1/2, -y+1/2, z'
> 43 '-z, y+1/2, -x+1/2'
> 44 '-z+1/2, y, -x+1/2'
> 45 '-z+1/2, y+1/2, -x'
> 46 '-y, x+1/2, -z+1/2'
> 47 '-y+1/2, x, -z+1/2'
> 48 '-y+1/2, x+1/2, -z'
> 49 '-x, z+1/2, -y+1/2'
> 50 '-x+1/2, z, -y+1/2'
> 51 '-x+1/2, z+1/2, -y'
> 52 '-z, x+1/2, -y+1/2'
> 53 '-z+1/2, x, -y+1/2'
> 54 '-z+1/2, x+1/2, -y'
> 55 '-y, z+1/2, -x+1/2'
> 56 '-y+1/2, z, -x+1/2'
> 57 '-y+1/2, z+1/2, -x'
> 58 '-x, y+1/2, -z+1/2'
> 59 '-x+1/2, y, -z+1/2'
> 60 '-x+1/2, y+1/2, -z'
> 61 'z, -y+1/2, -x+1/2'
> 62 'z+1/2, -y, -x+1/2'
> 63 'z+1/2, -y+1/2, -x'
> 64 'y, -x+1/2, -z+1/2'
> 65 'y+1/2, -x, -z+1/2'
> 66 'y+1/2, -x+1/2, -z'
> 67 'x, -z+1/2, -y+1/2'
> 68 'x+1/2, -z, -y+1/2'
> 69 'x+1/2, -z+1/2, -y'
> 70 'z, -x+1/2, -y+1/2'
> 71 'z+1/2, -x, -y+1/2'
> 72 'z+1/2, -x+1/2, -y'
> 73 'y, -z+1/2, -x+1/2'
> 74 'y+1/2, -z, -x+1/2'
> 75 'y+1/2, -z+1/2, -x'
> 76 'x, -y+1/2, -z+1/2'
> 77 'x+1/2, -y, -z+1/2'
> 78 'x+1/2, -y+1/2, -z'
> 79 'z, y+1/2, x+1/2'
> 80 'z+1/2, y, x+1/2'
> 81 'z+1/2, y+1/2, x'
> 82 'y, x+1/2, z+1/2'
> 83 'y+1/2, x, z+1/2'
> 84 'y+1/2, x+1/2, z'
> 85 'x, z+1/2, y+1/2'
> 86 'x+1/2, z, y+1/2'
> 87 'x+1/2, z+1/2, y'
> 88 'z, x+1/2, y+1/2'
> 89 'z+1/2, x, y+1/2'
> 90 'z+1/2, x+1/2, y'
> 91 'y, z+1/2, x+1/2'
> 92 'y+1/2, z, x+1/2'
> 93 'y+1/2, z+1/2, x'
> 94 'x, y+1/2, z+1/2'
> 95 'x+1/2, y, z+1/2'
> 96 'x+1/2, y+1/2, z'
> loop_
> _atom_type_symbol
> _atom_type_oxidation_number
> As3- -3
> Ga3+ 3
> loop_
> _atom_site_label
> _atom_site_type_symbol
> _atom_site_symmetry_multiplicity
> _atom_site_Wyckoff_symbol
> _atom_site_fract_x
> _atom_site_fract_y
> _atom_site_fract_z
> _atom_site_occupancy
> _atom_site_attached_hydrogens
> Ga1 Ga3+ 4 a 0 0 0 1. 0
> As2 As3- 4 c 0.25 0.25 0.25 1. 0
>
> #End of data_43359-ICSD
>
>
>
> --
> Allen Hall
> aj...@gm...
> al...@il...
>
>
>
> _______________________________________________
> xrayutilities-users mailing list
> xra...@li...
> https://lists.sourceforge.net/lists/listinfo/xrayutilities-users
>
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