Hi Albert, I don't check carefully, but I think the first one in the list of hall symbols for a space group type (among 230) is the standard one.
Togo On Mon, Aug 25, 2014 at 10:44 PM, Defusco III, Albert A <[email protected]> wrote: > Togo, > > That works perfectly. I'll keep you informed of my progress. Would it be > appropriate to set a default axis and origin for each space group if the user > is uncertain of which to chose? > > > Thanks, > Albert > > On Aug 22, 2014, at 7:56 PM, Atsushi Togo <[email protected]> wrote: > >> Hi, >> >> In spglib, I implemented a function to access symmetry operations of >> 'conventional' unit cell using the index of hall symbol. It's up to >> the Avogadro development strategy if Avogadro uses this function or >> not. Avogadro may wait for the fix in openbabel. >> >> The code is found at >> >> https://github.com/atztogo/spglib/releases/tag/v1.6.2 >> >> The function is as follows: >> >> /* Space-group operations in built-in database are accessed by index */ >> /* of hall symbol. The index is defined as number from 1 to 530. */ >> /* The muximum number of symmetry operations is 192. */ >> int spg_get_symmetry_from_database(int rotations[192][3][3], >> double translations[192][3], >> const int hall_number); >> >> I think there is no definition of index number of hall symbol. So the >> hall_number used in spglib is considered as just a local definition. >> If you prepare (graphical) user interface, the hall_number should be >> generated from a space group type with its setting of axes and origin. >> >> Togo >> >> On Fri, Aug 22, 2014 at 12:53 AM, Defusco III, Albert A >> <[email protected]> wrote: >>> Hi Togo, >>> >>> Yes, I meant non-primitive translation. For now I would prefer to retrieve >>> this information from Spglib to avoid replication errors. I can have >>> Avogadro translate a Hall symbol to the Hall number used in spg_database.c. >>> >>> Dealing with International symbols and non-primitive unit cells could be >>> troublesome, but I could always just force the user to choose an origin. >>> >>> >>> Thanks, >>> Albert >>> >>> >>> On Aug 20, 2014, at 7:57 PM, Atsushi Togo <[email protected]> wrote: >>> >>>> Hi, >>>> >>>> If you mean origin_shift as non primitive translation part of space >>>> group operations, I can understand what you wrote. I can extend spglib >>>> so that the database is accessed from the API. The other option is >>>> just to hard code the database in Avogadro's crystallography extension >>>> itself. It may be a matter of strategy. If Avogadro may have a chance >>>> to use other crystal symmetry libraries in the future, it may be >>>> better the later option. >>>> >>>> Togo >>>> >>>> On Thu, Aug 21, 2014 at 6:06 AM, Defusco III, Albert A <[email protected]> >>>> wrote: >>>>> Good afternoon everyone, >>>>> >>>>> I am working on getting porting the crystallography extension and space >>>>> group support into Avogadro 2. What is missing from Avogadro 2 is a >>>>> look-up of rotation matrices and origin shift vectors for a given space >>>>> group. Do you believe it is possible to extend Sgplib so that I can get >>>>> these quantities when specifying just the space group (either Hall >>>>> symbol/number or international symbol/number)? >>>>> >>>>> >>>>> Here's what I've done so far >>>>> >>>>> 1. I have added support for rotation matrices and origin shift vectors in >>>>> Avogado2's UnitCell class and added a fillUnitCell method to >>>>> crystaltools.cpp. A filled unit cell can then be given the the Spglib >>>>> routines for further action. (The rotation matrices and origin shift >>>>> vectors are only available if read from a cml file where they have been >>>>> specified in <transform3> child nodes of <symmetry>.) >>>>> >>>>> 2. Once a filled unit cell is generated all AvoSpglib/Spglib routines are >>>>> nearly unchanged when ported into Avogadro2. >>>>> >>>>> >>>>> >>>>> Here's an example of what I mean. >>>>> >>>>> int numRotations = get_rotation(int HallNumber, >>>>> int rotation[][3][3], >>>>> double origin_shift[][3]) >>>>> >>>>> HallNumber is read as input and rotation and origin_shift are populated >>>>> on output.The length of the rotation and origin_shift arrays is >>>>> numRotations. >>>>> >>>>> Using the space group "F 4d 2 3 -1d" (#525) there are 192 rotation >>>>> matrices and origin shift vectors. >>>>> >>>>> >>>>> >>>>> Thanks, >>>>> Albert >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------ >>>>> Albert DeFusco, Ph.D. >>>>> Research Assistant Professor >>>>> Technical Director, Center for Simulation and Modeling >>>>> University of Pittsburgh >>>>> Pittsburgh, PA 15260 >>>>> 412-648-3094 >>>>> http://www.sam.pitt.edu >>>>> >>>> >>>> >>>> >>>> -- >>>> Atsushi Togo >>>> http://atztogo.github.com/ >>>> [email protected] >>> >> >> >> >> -- >> Atsushi Togo >> http://atztogo.github.com/ >> [email protected] > -- Atsushi Togo http://atztogo.github.com/ [email protected] ------------------------------------------------------------------------------ Slashdot TV. Video for Nerds. Stuff that matters. http://tv.slashdot.org/ _______________________________________________ Avogadro-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/avogadro-devel
