[cctbxbb] Niggli-reduced cell C++ implementation
Ralf Grosse-Kunstleve
rwgrosse-kunstleve at lbl.gov
Tue Apr 24 12:42:45 PDT 2012
Hi Martin,
Based on
iotbx.lattice_symmetry --unit_cell="4.630811 4.630811 4.630811 90 90 90"
and
iotbx.lattice_symmetry --unit_cell="3.27448 5.67156 5.67156 99.5941 106.779
90"
the first unit cell is (obviously) cubic, the second is only monoclinic.
Even with
iotbx.lattice_symmetry --unit_cell="3.27448 5.67156 5.67156 99.5941 106.779
90" --delta=20
it only comes back as orthorhombic.
Is this what you expect?
Ralf
On Tue, Apr 24, 2012 at 10:57 AM, Martin Uhrin <martin.uhrin.10 at ucl.ac.uk>wrote:
> Dear cctbxers,
>
> I've finally found the time to play around with a C++ version of the KG
> algorithm and I've come across a result I don't understand. I've tried
> both David's C++ and the cctbx python niggli_cell() implementations and
> they both give the roughly the same answer.
>
> I'm reducing the following cell with two, equivalent, representations (a,
> b, c, alpha, beta, gamma):
>
> Before:
>
> 1: 4.630811 4.630811 4.630811 90 90 90
> 2: 3.27448 5.67156 5.67156 99.5941 106.779 90
>
> After:
>
> 1: 4.63081 4.63081 4.63081 90 90 90
> 2: 3.27448 5.67154 5.67156 99.5941 90 106.778
>
> Looking at the trace, cell 1 undergoes step 3 and finishes while cell 2
> undergoes steps 2, 3, 7 and 4.
>
> Does anyone know why these haven't converged to the same cell?
>
> Many thanks,
> -Martin
>
> On 23 March 2012 17:12, Ralf Grosse-Kunstleve <rwgrosse-kunstleve at lbl.gov>wrote:
>
>> Hi Martin,
>> Let me know if you need svn write access to check in your changes. All I
>> need is your sourceforge user id.
>> Ralf
>>
>>
>> On Fri, Mar 23, 2012 at 3:35 AM, Martin Uhrin <martin.uhrin.10 at ucl.ac.uk>wrote:
>>
>>> Dear David and Rolf,
>>>
>>> thank you for your encouragement.
>>>
>>> David: I'm more than happy to port your implementation to cctbx if
>>> you're happy with this. Of course I don't want to step on your toes so if
>>> you'd rather do it yourself (or not at all) that's cool.
>>>
>>> There may be some licensing issues to sort out as it looks like cctbx
>>> has a custom (non viral) license but the BSD license is likely compatible.
>>>
>>> On first impression I think a new class would be the way to go but I'd
>>> have to look at the two algorithms in greater detail to be sure.
>>>
>>> All the best,
>>> -Martin
>>>
>>>
>>> On 22 March 2012 22:00, Ralf Grosse-Kunstleve <
>>> rwgrosse-kunstleve at lbl.gov> wrote:
>>>
>>>> Hi Martin,
>>>> You're very welcome to add a C++ version of the Krivy-Gruber algorithm
>>>> to cctbx if that's what you had in mind.
>>>> I'm not sure what's better, generalizing the fast-minimum-reduction
>>>> code, or just having an independent implementation.
>>>> Ralf
>>>>
>>>> On Thu, Mar 22, 2012 at 2:24 PM, Martin Uhrin <
>>>> martin.uhrin.10 at ucl.ac.uk> wrote:
>>>>
>>>>> Dear Cctbx community,
>>>>>
>>>>> Firstly I'd like to say thank you to Rolf, Nicholas and Paul for their
>>>>> expertly thought through implementation of the reduced cell algorithm.
>>>>> I've found it to be extremely useful for my work.
>>>>>
>>>>> My code is all in C++ and I'd like to be able to use the Krivy-Gruber
>>>>> algorithm. My understanding is that only the reduced (Buerger) unit cell
>>>>> algorithm is implemented in C++ [1] which guarantees shortest lengths but
>>>>> not unique angles. From my understanding the Krivy-Gruber would also
>>>>> guarantee me uniqueness of unit cell angles, however this is only
>>>>> implemented in Python [2]. Sorry to be so verbose, I just wanted to check
>>>>> that I was on the right page.
>>>>>
>>>>> Would it be possible for me to implement the Krivy-Gruber in C++ by
>>>>> adding in the epsilon_relative to the parameter and following the procedure
>>>>> found in the python version?
>>>>>
>>>>> Many thanks,
>>>>> -Martin
>>>>>
>>>>> [1]
>>>>> http://cctbx.sourceforge.net/current/c_plus_plus/classcctbx_1_1uctbx_1_1fast__minimum__reduction.html
>>>>> [2]
>>>>> http://cctbx.sourceforge.net/current/python/cctbx.uctbx.krivy_gruber_1976.html
>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Martin Uhrin Tel: +44
>>>>> 207 679 3466
>>>>> Department of Physics & Astronomy Fax:+44 207 679 0595
>>>>> University College London
>>>>> martin.uhrin.10 at ucl.ac.uk
>>>>> Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk
>>>>>
>>>>> _______________________________________________
>>>>> cctbxbb mailing list
>>>>> cctbxbb at phenix-online.org
>>>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>>>
>>>>>
>>>>
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>>>>
>>>
>>>
>>> --
>>> Martin Uhrin Tel: +44
>>> 207 679 3466
>>> Department of Physics & Astronomy Fax:+44 207 679 0595
>>> University College London
>>> martin.uhrin.10 at ucl.ac.uk
>>> Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk
>>>
>>> _______________________________________________
>>> cctbxbb mailing list
>>> cctbxbb at phenix-online.org
>>> http://phenix-online.org/mailman/listinfo/cctbxbb
>>>
>>>
>>
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>>
>
>
> --
> Martin Uhrin Tel: +44
> 207 679 3466
> Department of Physics & Astronomy Fax:+44 207 679 0595
> University College London
> martin.uhrin.10 at ucl.ac.uk
> Gower St, London, WC1E 6BT, U.K. http://www.cmmp.ucl.ac.uk
>
> _______________________________________________
> cctbxbb mailing list
> cctbxbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/cctbxbb
>
>
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