"""AiiDA-Supecell plugin -- Supercell Parser"""
from collections import defaultdict
from pymatgen.core import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from aiida.common import exceptions
from aiida.parsers import Parser
from aiida import orm
from aiida.engine import ExitCode
from aiida_supercell.utils import parse_supercell_output
[docs]class SupercellParser(Parser):
"""Parser for Supercell Calculations"""
[docs] def parse(self, **kwargs):
"""Receives in input a dictionary of retrieved nodes. Does all the logic here.
"""
try:
_ = self.retrieved
except exceptions.NotExistent:
return self.exit_codes.ERROR_NO_RETRIEVED_FOLDER
exit_code = self._parse_stdout()
if exit_code is not None:
return exit_code
return ExitCode(0)
[docs] def _parse_stdout(self): # pylint: disable=too-many-locals
"""Supercell Basic Output parser"""
fname = self.node.get_attribute('output_filename')
if fname not in self.retrieved.list_object_names():
return self.exit_codes.ERROR_OUTPUT_STDOUT_MISSING
try:
output_string = self.retrieved.get_object_content(fname)
except IOError:
return self.exit_codes.ERROR_OUTPUT_STDOUT_READ
output_list = self.retrieved.list_object_names(path='Output')
enrg_outputs = []
for o in output_list:
if 'aiida_supercell_coulomb_energy_' in o:
enrg_outputs.append(o)
result_dict = parse_supercell_output(output_string)
s_dict = defaultdict(dict)
res_dict = defaultdict(lambda: defaultdict(lambda: defaultdict(dict)))
if len(enrg_outputs) > 0:
res_dict['coulombic_energy_unit'] = 'eV'
enrg_content = ''
for item in enrg_outputs:
enrg_content += self.retrieved.get_object_content(item)
for i in enrg_content.split('\n')[:-1]:
sp = i.split()
enrg = float(sp[1])
label = sp[0].split('_')[2]
res_dict['Structures_info'][label]['coulombic_energy'] = enrg
for s in output_list:
if s[-3:] == 'cif':
sp = s.split('_')
label = sp[2]
degneracy = sp[-1].split('.')[0][1:]
s_content = self.retrieved.get_object_content(f'Output/{s}')
s_pmg = Structure.from_str(s_content, fmt='cif')
s_pmg.sort()
spg = SpacegroupAnalyzer(s_pmg)
res_dict['Structures_info'][label]['degeneracy'] = int(degneracy)
res_dict['Structures_info'][label]['crystal_system'] = spg.get_crystal_system()
res_dict['Structures_info'][label]['lattice_type'] = spg.get_lattice_type()
res_dict['Structures_info'][label]['space_group_symbol'] = spg.get_space_group_symbol()
s_dict[label] = orm.StructureData(pymatgen_structure=s_pmg)
result_dict.update(res_dict)
self.out('output_parameters', orm.Dict(dict=result_dict))
for key, value in s_dict.items():
self.out(f'output_structures.{key}', value)
return None
#EOF