[ase-users] VASP module in ASE

[Jussi Enkovaara]

Jonas Björk wrote:
>> Let's say I want to do 256 water molecules, and the order is
>> HHOHHOHHOHHO ..., then I will also get a HUGE POTCAR file.  I think it
>> would be best if the ASE Vasp interface could be intelligent and reorder
>> things so that the POTCAR file only has two setups.
> 
> I agree, lets do it this way.

Hi,
if you look how I was constructing POSCAR and POTCAR (svn revision 508) one should 
get in the above example POTCAR with only two setups:

First I was construcytig a dictionary of atomic species, where the key is the 
atomic symbol and value the number of this species:

         # Determine the number of atomic species
         self.symbols = {}
         for atom in atoms:
             symbol = atom.get_symbol()
             if not self.symbols.has_key(symbol):
                 self.symbols[symbol] = 1
             else:
                 self.symbols[symbol] += 1


POTCAR can then be constructed just with loop over symbols:

         for symbol in self.symbols:
             try:
                 name = symbol + '_' + p['setups'][symbol]
             except (TypeError, KeyError):
                 name = symbol
             name += '/POTCAR.Z'
             found = False
             for path in pppaths:
                 filename = join(path, name)
                 if isfile(filename) or islink(filename):
                     found = True
                     self.ppp_list.append(filename)
                     break
             if not found:
                 raise RuntimeError('No pseudopotential for %s!' % symbol)


After writing the unit cell information in POSCAR, the number of atomic species can 
be written:

         for nspecies in self.symbols.values():
             poscar.write('%i ' % nspecies)
         poscar.write('\n')

and the actual positions:

         for symbol in self.symbols.keys():
             mask = [asymbol == symbol for asymbol in self.all_symbols]
             ind = npy.asarray(mask, bool)
             for pos in self.positions[ind]:
                 poscar.write('%.14f %.14f %.14f\n' %  tuple(pos))

I do not know if this is the optimal way, but it seemed to be working.

Best regards,
Jussi