Re: Computing code for hkl generation [pyobjcryst]

[Simon Billinge]

thanks so much for sharing, Vincent, just what I was after!

S

On Sat, Jul 24, 2021 at 6:25 AM  wrote:

> Dear all,
>
> Late answer but yes, you can easily script HKL generation and single
> crystal Fhkl in pyobjcryst from python.
>
> See the example notebook on google colab:
>
>
> https://colab.research.google.com/drive/1dGMPWJgfKrR7UYOnSyQtHuZDdVyUXcfx?usp=sharing
>
> (you need to log in and run all cells - first time is slow as it compiles
> libobjcryst and pyobjcryst in the first cell).
>
> And yes, pyobjcryst can also be used for powder diffraction, including
> indexing and structure solution. See other example at:
>
> https://colab.research.google.com/drive/1qVnqteKAp2GRMEYS8g4VX61DVCvOPzik?usp=sharing
>
>
> There are more examples in the pyobjcryst sources from
> https://github.com/diffpy/pyobjcryst (or
> https://github.com/vincefn/pyobjcryst).
>
> Best regards,
> Vincent
>
> Le 18 juil. 2021 à 21:59, Simon Billinge  a écrit :
>
> FOX can do this (http://fox.vincefn.net/Manual/Powder) and ObjCryst,
> which is the engine beyond FOX, has python bindings (look for pyobjcryst).
>
> I am not sure if there is an example of how to use pyobjcryst to do this,
> or if it is even possible, but it seems as if it would be a good thing to
> look into. Vincent Favre-Nicolin would know if he is monitoring this list...
>
> S
>
> On Sun, Jul 18, 2021 at 3:45 PM JR  wrote:
>
>> Dear Martin,
>>
>> try CCTBX, https://cci.lbl.gov/cctbx_docs/
>>
>> Jan
>>
>> Dne 18. 7. 2021 18:03 napsal uživatel "Etter, Martin" <
>> martin.et...@desy.de>:
>>
>> Dear Colleagues,
>>
>> I am currently looking for a Python or C/C++ module or function which
>> generates hkl reflections with the correct systematic absences by giving
>> the space group number or symbol to it. Is anybody aware, if there are open
>> source modules exisiting already, before I start to write it by myself?
>> If not I would appreciate also, if there are hints on optimized code for
>> this problem, as I would like to write a time-saving algorithm.
>>
>> With kind regards from Hamburg,
>>
>> Martin Etter
>>
>> ++
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>> ++
>>
>>
>> ++
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>> ++
>>
>>
>
> --
> Simon Billinge
> Professor, Columbia University
> Physicist, Brookhaven National Laboratory
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> ++
>
>
> —
> Vincent Favre-Nicolin
>
>
>
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> ++
>
>

-- 
Simon Billinge
Professor, Columbia University
Physicist, Brookhaven National Laboratory
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Re: Computing code for hkl generation [pyobjcryst]

[vincefn]

Dear all,

Late answer but yes, you can easily script HKL generation and single 
crystal Fhkl in pyobjcryst from python.

See the example notebook on google colab:

https://colab.research.google.com/drive/1dGMPWJgfKrR7UYOnSyQtHuZDdVyUXcfx?usp=sharing
 


(you need to log in and run all cells - first time is slow as it compiles 
libobjcryst and pyobjcryst in the first cell).

And yes, pyobjcryst can also be used for powder diffraction, including 
indexing and structure solution. See other example at:
https://colab.research.google.com/drive/1qVnqteKAp2GRMEYS8g4VX61DVCvOPzik?usp=sharing
 

 

There are more examples in the pyobjcryst sources from 
https://github.com/diffpy/pyobjcryst  (or 
https://github.com/vincefn/pyobjcryst ).

Best regards,
Vincent

> Le 18 juil. 2021 à 21:59, Simon Billinge  > a écrit :
> 
> FOX can do this (http://fox.vincefn.net/Manual/Powder 
> ) and ObjCryst, which is the engine 
> beyond FOX, has python bindings (look for pyobjcryst).
> 
> I am not sure if there is an example of how to use pyobjcryst to do this, or 
> if it is even possible, but it seems as if it would be a good thing to look 
> into. Vincent Favre-Nicolin would know if he is monitoring this list...
> 
> S
> 
> On Sun, Jul 18, 2021 at 3:45 PM JR mailto:rohli...@fzu.cz>> 
> wrote:
> Dear Martin,
> 
> try CCTBX, https://cci.lbl.gov/cctbx_docs/ 
> 
> Jan
> 
> Dne 18. 7. 2021 18:03 napsal uživatel "Etter, Martin"  >:
> Dear Colleagues, 
> 
> I am currently looking for a Python or C/C++ module or function which 
> generates hkl reflections with the correct systematic absences by giving the 
> space group number or symbol to it. Is anybody aware, if there are open 
> source modules exisiting already, before I start to write it by myself? 
> If not I would appreciate also, if there are hints on optimized code for this 
> problem, as I would like to write a time-saving algorithm. 
> 
> With kind regards from Hamburg, 
> 
> Martin Etter
> 
> ++ 
> Please do NOT attach files to the whole list  > 
> Send commands to mailto:lists...@ill.fr>> eg: HELP as the 
> subject with no body text 
> The Rietveld_L list archive is on 
> http://www.mail-archive.com/rietveld_l@ill.fr/ 
>  
> ++ 
> 
> 
> ++
> Please do NOT attach files to the whole list  >
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> subject with no body text
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> 
> ++
> 
> 
> 
> -- 
> Simon Billinge
> Professor, Columbia University
> Physicist, Brookhaven National Laboratory
> ++
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> The Rietveld_L list archive is on 
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> 
> ++
> 

— 
Vincent Favre-Nicolin



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Re: Computing code for hkl generation

[Martin Etter]

Dear Colleagues,

many thanks for your great recommendations, actually some algorithms 
already helped me a lot.


With kind regards from Hamburg,

Martin


Am 18.07.2021 um 18:03 schrieb Etter, Martin:

Dear Colleagues,

I am currently looking for a Python or C/C++ module or function which generates 
hkl reflections with the correct systematic absences by giving the space group 
number or symbol to it. Is anybody aware, if there are open source modules 
exisiting already, before I start to write it by myself?
If not I would appreciate also, if there are hints on optimized code for this 
problem, as I would like to write a time-saving algorithm.

With kind regards from Hamburg,

Martin Etter

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Re: Computing code for hkl generation

[Jonathan WRIGHT]

Dear Martin,

In addition to the other replies:


I am currently looking for a Python


xfab does this, see:

https://github.com/FABLE-3DXRD/xfab/blob/fd3015dbd4145daf6a471765887c3aa139eb8bab/xfab/tools.py#L1039


  or C/C++ module


sginfo (https://github.com/rwgk/sginfo) offers a "simple_hkllist" option.

Best,

Jon


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Re: Computing code for hkl generation

[Toby, Brian H.]

Sure.

This can be done in GSAS-II from the GUI (see 
https://subversion.xray.aps.anl.gov/pyGSAS/Tutorials/Simulation/SimTutorial.htm,
 just export a HKL file rather than a simulated pattern) or from a Python 
script (see 
https://gsas-ii.readthedocs.io/en/latest/GSASIIscriptable.html#pattern-simulation,
 note this example writes both reflections and a simulated pattern.)

Those examples use a CIF as input, but if all that is wanted would be 
reflections, it is possible to define a phase using a space group (which can be 
a non-standard setting), unit cell dimensions and a single dummy atom position 
as input.

Brian

On Jul 18, 2021, at 3:13 PM, Gallington, Leighanne C. 
mailto:galling...@anl.gov>> wrote:

I would think GSAS-II might also have something.  Maybe Brian Toby can chime in?

Get Outlook for Android<https://aka.ms/AAb9ysg>


From: rietveld_l-requ...@ill.fr<mailto:rietveld_l-requ...@ill.fr> 
mailto:rietveld_l-requ...@ill.fr>> on behalf of 
Simon Billinge mailto:sb2...@columbia.edu>>
Sent: Sunday, July 18, 2021, 3:01 PM
To: JR
Cc: Etter, Martin; Rietveld
Subject: Re: Computing code for hkl generation

FOX can do this (http://fox.vincefn.net/Manual/Powder) and ObjCryst, which is 
the engine beyond FOX, has python bindings (look for pyobjcryst).

I am not sure if there is an example of how to use pyobjcryst to do this, or if 
it is even possible, but it seems as if it would be a good thing to look into. 
Vincent Favre-Nicolin would know if he is monitoring this list...

S

On Sun, Jul 18, 2021 at 3:45 PM JR mailto:rohli...@fzu.cz>> 
wrote:
Dear Martin,

try CCTBX, https://cci.lbl.gov/cctbx_docs/

Jan

Dne 18. 7. 2021 18:03 napsal uživatel "Etter, Martin" 
mailto:martin.et...@desy.de>>:

Dear Colleagues,

I am currently looking for a Python or C/C++ module or function which generates 
hkl reflections with the correct systematic absences by giving the space group 
number or symbol to it. Is anybody aware, if there are open source modules 
exisiting already, before I start to write it by myself?
If not I would appreciate also, if there are hints on optimized code for this 
problem, as I would like to write a time-saving algorithm.

With kind regards from Hamburg,

Martin Etter

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--
Simon Billinge
Professor, Columbia University
Physicist, Brookhaven National Laboratory


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Re: Computing code for hkl generation

[Gallington, Leighanne C.]

I would think GSAS-II might also have something.  Maybe Brian Toby can chime in?

Get Outlook for Android<https://aka.ms/AAb9ysg>


From: rietveld_l-requ...@ill.fr  on behalf of Simon 
Billinge 
Sent: Sunday, July 18, 2021, 3:01 PM
To: JR
Cc: Etter, Martin; Rietveld
Subject: Re: Computing code for hkl generation

FOX can do this (http://fox.vincefn.net/Manual/Powder) and ObjCryst, which is 
the engine beyond FOX, has python bindings (look for pyobjcryst).

I am not sure if there is an example of how to use pyobjcryst to do this, or if 
it is even possible, but it seems as if it would be a good thing to look into. 
Vincent Favre-Nicolin would know if he is monitoring this list...

S

On Sun, Jul 18, 2021 at 3:45 PM JR mailto:rohli...@fzu.cz>> 
wrote:
Dear Martin,

try CCTBX, https://cci.lbl.gov/cctbx_docs/

Jan

Dne 18. 7. 2021 18:03 napsal uživatel "Etter, Martin" 
mailto:martin.et...@desy.de>>:

Dear Colleagues,

I am currently looking for a Python or C/C++ module or function which generates 
hkl reflections with the correct systematic absences by giving the space group 
number or symbol to it. Is anybody aware, if there are open source modules 
exisiting already, before I start to write it by myself?
If not I would appreciate also, if there are hints on optimized code for this 
problem, as I would like to write a time-saving algorithm.

With kind regards from Hamburg,

Martin Etter

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--
Simon Billinge
Professor, Columbia University
Physicist, Brookhaven National Laboratory

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Re: Computing code for hkl generation

[Simon Billinge]

FOX can do this (http://fox.vincefn.net/Manual/Powder) and ObjCryst, which
is the engine beyond FOX, has python bindings (look for pyobjcryst).

I am not sure if there is an example of how to use pyobjcryst to do this,
or if it is even possible, but it seems as if it would be a good thing to
look into. Vincent Favre-Nicolin would know if he is monitoring this list...

S

On Sun, Jul 18, 2021 at 3:45 PM JR  wrote:

> Dear Martin,
>
> try CCTBX, https://cci.lbl.gov/cctbx_docs/
>
> Jan
>
> Dne 18. 7. 2021 18:03 napsal uživatel "Etter, Martin" <
> martin.et...@desy.de>:
>
> Dear Colleagues,
>
> I am currently looking for a Python or C/C++ module or function which
> generates hkl reflections with the correct systematic absences by giving
> the space group number or symbol to it. Is anybody aware, if there are open
> source modules exisiting already, before I start to write it by myself?
> If not I would appreciate also, if there are hints on optimized code for
> this problem, as I would like to write a time-saving algorithm.
>
> With kind regards from Hamburg,
>
> Martin Etter
>
> ++
> Please do NOT attach files to the whole list 
>
> Send commands to  eg: HELP as the subject with no body
> text
> The Rietveld_L list archive is on
> http://www.mail-archive.com/rietveld_l@ill.fr/
> ++
>
>
> ++
> Please do NOT attach files to the whole list  >
> Send commands to  eg: HELP as the subject with no body
> text
> The Rietveld_L list archive is on
> http://www.mail-archive.com/rietveld_l@ill.fr/
> ++
>
>

-- 
Simon Billinge
Professor, Columbia University
Physicist, Brookhaven National Laboratory
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Re: Computing code for hkl generation

[JR]

Dear Martin,try CCTBX, https://cci.lbl.gov/cctbx_docs/JanDne 18. 7. 2021 18:03 napsal uživatel "Etter, Martin" :Dear Colleagues,



I am currently looking for a Python or C/C++ module or function which generates hkl reflections with the correct systematic absences by giving the space group number or symbol to it. Is anybody aware, if there are open source modules exisiting already, before I start to write it by myself?

If not I would appreciate also, if there are hints on optimized code for this problem, as I would like to write a time-saving algorithm.



With kind regards from Hamburg,



Martin Etter

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Re: Computing code for hkl generation

[Roberto de Avillez]

Hi Martin,

You may consider these projects, but I don't know them very well.

PyXRD 0.8.4  https://pypi.org/project/PyXRD/
X-ray utilities  https://xrayutilities.sourceforge.io/index.html

Roberto de Avillez


Em dom., 18 de jul. de 2021 às 13:03, Etter, Martin 
escreveu:

> Dear Colleagues,
>
> I am currently looking for a Python or C/C++ module or function which
> generates hkl reflections with the correct systematic absences by giving
> the space group number or symbol to it. Is anybody aware, if there are open
> source modules exisiting already, before I start to write it by myself?
> If not I would appreciate also, if there are hints on optimized code for
> this problem, as I would like to write a time-saving algorithm.
>
> With kind regards from Hamburg,
>
> Martin Etter
> ++
> Please do NOT attach files to the whole list  >
> Send commands to  eg: HELP as the subject with no body
> text
> The Rietveld_L list archive is on
> http://www.mail-archive.com/rietveld_l@ill.fr/
> ++
>
>
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