def structure2aSys(structure,idoffset=1):
"""
Converts Structure object of pymatgen to NAPSystem object in nap.
Args:
structure (Structure): pymatgen Structure object to be converted
to NAPSystem object..
Returns:
aSys (NAPSystem):
"""
lattice= structure.lattice
alc= 1.0
a1= np.array(lattice.matrix[0])
a2= np.array(lattice.matrix[1])
a3= np.array(lattice.matrix[2])
#... rescale a? vectors
a1= a1/alc
a2= a2/alc
a3= a3/alc
aSys= NAPSystem()
aSys.set_lattice(alc,a1,a2,a3)
for ia in range(structure.num_sites):
ai= Atom()
si= structure[ia]
crd= si.frac_coords
ai.set_pos(crd[0],crd[1],crd[2])
sid= structure.symbol_set.index(si.species_string)+idoffset
ai.set_sid(sid)
ai.set_id(ia+1)
aSys.add_atom(ai)
return aSys
def doc_to_pos(doc, conf):
"""
Make a pos file, which has pmd format, from a document in MongoDB.
"""
psys = NAPSystem()
matrix = doc['calculations'][-1]['output']['crystal']['lattice']['matrix']
a1 = matrix[0]
a2 = matrix[1]
a3 = matrix[2]
psys.set_lattice(1.0, a1, a2, a3)
species_ids = conf['species_ids']
sites = doc['calculations'][-1]['output']['crystal']['sites']
for site in sites:
ra = site['abc']
ai = Atom()
ai.set_pos(ra[0], ra[1], ra[2])
ai.set_sid(species_ids[site['species'][0]['element']])
psys.add_atom(ai)
return psys
