[ase-users] ase Atoms methods

[Jens Jørgen Mortensen]

On Wed, 2008-09-24 at 10:08 +0300, Pekka Koskinen wrote:
> Dear Jens,
> 
> I've sub-classed ase.Atoms, having some additional methods I've found
> convenient. They have been convenient to use both with the
> tight-binding code HOTBIT, as well as with GPAW (post-processing).
> Below I list some of them, and the description of what they do. It
> would be nice it you could consider implementing, at least some of
> them, to ase.Atoms.
> 
> Suggestions:
> ==========
> 
> * get_name(name) / set_name()
> With set_name('benzene') you may give the atoms a name 'benzene'. With
> get_name() you get it, and if it is not set, the name is by default
> the chemical formula 'C6H6' (this would be taken by compressing the
> list of chemical symbols). This method has been handy, e.g. for naming
> output files for post-processing (Naming becomes automatic and
> self-explanatory; and there is often no need to change old output
> files for new systems.) 
> 
> * get_cell_axes()
> I frequently need, for orthorhombic cells (which is often the case)
> only the cell axes. These usually need to be taken from the 3x3 matrix
> that get_cell gives (requiring one line more code). This method gives
> only the lengths of the axes as an array.
> 
> * reduce_atoms_into_cell()
> Move atoms so that all atoms are within the unit cell. Convenient for
> plotting (If a non-orthorhombic minimal unit cell is more natural to
> be used in constructing the supercell.)
> 
> * get_vector(ri,rj,mic=True/False)
> Return the vector from ri to rj, either using minimum image convention
> or not. Both ri and rj can be integers (atom indices) or arbitrary
> position arrays. This allows flexible measuring of distances within
> your (periodic) cell.
> 
> * get_distance(ri,rj,mic=True/False)
> The same as the existing get_distance, but either ri or rj, or both
> can also be position arrays, like above.
> 
> * get_size()
> Get the spatial extent of the atoms (cluster) in all directions; i.e.
> array( [max(x)-min(x),max(y)-min(y),max(z)-min(z)] ). This info is
> frequently needed in post-processing.
> 
> * get_kinetic_temperature(fixed=0)
> Transform kinetic energy into kinetic temperature; the kinetic
> temperature is always more informative than kinetic energy in eV's.
> With keyword fixed, you may provide the number degrees of freedom that
> should not contribute to kinetic temperature (i.e. T=ekin * 2 /
> ((3*N-fixed)*kB); for example for free clusters fixed should be 6
> (translations/rotations) ).
> 
> * get_moments_of_inertia(center=None)
> Return moments of inertia and principal axes wrt. given rotation
> center. If center==None, return them wrt. center of mass.
>  
> * set_array(name,a) /get_array(name)
> General-purpose methods to store and retrieve some data related to
> atoms. This type of method I end up missing frequently in GPAW
> calculations. This could descent into Atom-class as well, allowing
> e.g. 
> set_array('Bader charge',charge_array)
> for atom in atoms:
>     print atom.get_property('Bader charge')
> 
> 
> Some of these are 'convenience' methods, but at least I found many of
> them to be very convenient indeed. The implementations of all of these
> are quite easy, so I think the question is more if you want these in
> your Atoms. Better naming is welcome.
> 
> I attach also the source code. The implementations are old and not
> very elegant, but I did not want to work on them too much (in case you
> would be willing to adopt them). There are also methods related to
> bonding information (atom connectivity) that I suggested to include to
> ase some time ago, but I don't like the way I've done it, and there is
> space for improvement. 
> 
> If you have any questions or better suggestions regarding the methods
> above, I would be happy to discuss more.
> 
> Best regards,
> Pekka
> 
> 
> -- 
> Pekka Koskinen
> NanoScience Center
> University of Jyväskylä
> work/työ: +358 (0)14 260 4717
> handy/matkap.:+358 (0)40 356 4460
>