Hi David, On Wed, Mar 28, 2012 at 1:41 AM, David Lonie <[email protected]> wrote: > On Tue, Mar 27, 2012 at 11:35 AM, Albert DeFusco <[email protected]> wrote: >> David, >> >> After some playing around I was able to determine that SPGlib will generate >> the primitive lattice and basis atoms correctly for use in PWScf. The >> avospg method reduceToPrimitive appears to work correctly only when I >> disable spg_refine_cell. So far I have been unable to figure out what might >> be wrong between OBUnitCell::SetData and the Avogadro display. > > Interesting -- It sounds like refine cell may be converting the > primitive cell back to a conventional cell?
Yes. It reduces to a conventional unit cell. A primitive lattice of a conventional unit cell that has centring can be obtained by multiplying a transformation matrix that is referred to the International table of crystallography vol. A. Furthermore, when using spg_refine_cell, the crystallographic axes are redefined in Cartesian coordinates. So if the lattice vectors are stored in a 3x3 matrix in Cartesian coordinates, they may be re-oriented. This re-orientation does not happen in spg_find_primitive. Togo > >> What I would like to do is use the spglib and avospg (crystallography >> extension) methods to determine the primitive lattice from my PWScf input >> generator. The goal is have a button that will generate the PWScf input >> using either the generated primitive cell or take the displayed cell >> verbatim without changing the display. Is it possible to connect the >> crystallography extension with a quantum input generator or should I >> re-implement the necessary methods in the PWScf input generator? > > This sounds like a nice feature! My suggestion here would be to move > the avospg stuff into the main libavogadro library. That way both > extensions could use the functionality without having to maintain two > separate copies of spglib. > > Dave > > ------------------------------------------------------------------------------ > This SF email is sponsosred by: > Try Windows Azure free for 90 days Click Here > http://p.sf.net/sfu/sfd2d-msazure > _______________________________________________ > Avogadro-devel mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/avogadro-devel -- Atsushi Togo http://atztogo.users.sourceforge.net/ [email protected] ------------------------------------------------------------------------------ This SF email is sponsosred by: Try Windows Azure free for 90 days Click Here http://p.sf.net/sfu/sfd2d-msazure _______________________________________________ Avogadro-devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/avogadro-devel
