def _query(idn=None, formula=None):
"""Make the actual query."""
importer = CodDbImporter()
if idn is not None:
return importer.query(id=idn)
if formula is not None:
return importer.query(formula=formula)
return None
def _COD_search(self):
from .search.cod import cod_check
from aiida.tools.dbimporters.plugins.cod import CodDbImporter
"""
Deals with the retrieval of a structure
from the COD database, according to the request dictionary
Returns a database search object (array of arrays of structures)
"""
kwords = cod_check(Dict(dict=self.ctx.db))
self.ctx.db_valid = kwords.dict.valid
self.ctx.db_invalid = kwords.dict.invalid
# empty dictionary
if not bool(self.ctx.db_valid):
self.report('No valid keywords in search tag in json')
return self.exit_codes.ERROR_MISSING_KEY
# query the database for structures
importer = CodDbImporter()
self.ctx.allcifs = importer.query(**self.ctx.db_valid)
self.ctx.n_structures = len(self.ctx.allcifs)
if self.ctx.n_structures == 0:
self.report('No structure retrieved')
self.ctx.cif = None
return self.exit_codes.ERROR_NO_STRUCTURE
else:
s = self.ctx.allcifs[0].get_aiida_structure()
s.store()
self.ctx.cif = s
if self.ctx.n_structures >= 2:
self.report('{} structure satisfy the request'.format(
self.ctx.n_structures))
def create_spinel_structurelist():
from aiida.tools.dbimporters.plugins.cod import CodDbImporter
from icet.tools import get_primitive_structure
# Import the ordered MgAl2O4 from COD db
importer = CodDbImporter()
mgalo = importer.query(id=1010129)[0]
ase_mgalo = mgalo.get_ase_structure()
primitive_structure = get_primitive_structure(ase_mgalo)
chemical_symbols = [['Mg', 'Al'] for i in range(6)] + [['O']
for i in range(8)]
# The concentration of A is 2/14 \in (0.1428, 0.1429)
concentration_restrictions = {'Mg': (0.1428, 0.1429)}
ase_structurelist = []
for structure in enumerate_structures(
primitive_structure,
range(1, 3),
chemical_symbols,
concentration_restrictions=concentration_restrictions):
ase_structurelist.append(structure)
return ase_structurelist
def cod_query(cod_values):
"""
performs a search of any CIF structure that is provided
according to the data coming from the input JSON request
returns a list of structures and an error code if there is
something wrong with things
"""
qlist = cod_values.get_dict()
importer = CodDbImporter()
found = importer.query(**qlist)
found_list = found.fetch_all()
x = [i.source['id'] for i in found_list]
# returned list of retrieved structures
return List(list=x)
# 1010301,
1010348,
1010404,
1010406,
1010407,
1010419,
1010420,
1010424,
1010425,
1010652,
1010653,
]:
r = codi.query(id=entry)
cif = r[0].get_cif_node(store=True)
try:
struct = cif._get_aiida_structure(store=True)
except KeyError:
print('{}: unable to construct AiiDA structure -- structure '
'possibly contains deuterium'.format(entry))
continue
elements = parse_formula(cif.get_formulae()[0])
ecutwfc_max = 0
ecutrho_max = 0
try: