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] ------------------------------------------------------------------------------ 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
