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import httk
import httk.db
import os
from classes import DefectCell
from httk.atomistic import Structure
[docs]
def get_defect_cif(host_name, defect_name, db_path="../../defect/defects.sqlite", out_dir="cif_out"):
os.makedirs(out_dir, exist_ok=True)
backend = httk.db.backend.Sqlite(db_path)
store = httk.db.store.SqlStore(backend)
search = store.searcher()
search_defect = search.variable(DefectCell)
host_name = host_name + "_PBE"
search.add(search_defect.host_name == host_name)
search.output(search_defect, "defect")
saved_paths = []
i = 0
for match, _ in search:
defect_cell = match[0]
if not defect_cell.defect_name.startswith(defect_name):
continue
struct = defect_cell.defect_structure
# here we use the actual defect name (C_int0, C_int1,osv)
filename = f"{host_name}_{defect_cell.defect_name}.cif"
full_path = os.path.abspath(os.path.join(out_dir, filename))
httk.save(struct, full_path)
print(f"CIF saved: {full_path}")
saved_paths.append(full_path) # dont need now, maybe later
i += 1
backend.close()
return saved_paths
if __name__ == "__main__":
get_defect_cif(
host_name="As2",
defect_name="C_int",
db_path="../../defect/defects.sqlite",
out_dir="cif_out"
)