def cmd_import(filename, dry_run, fleurinp):
"""
Import a `StructureData` from a Fleur input file.
FILENAME is the name/path of the inp.xml file to use.
If you want to import a structure from any file type you can use
'verdi data structure import -ase <filename>' instead.
"""
from aiida_fleur.data.fleurinp import FleurinpData
if not filename.endswith('.xml'):
echo.echo_critical(
'Error: Currently, only StructureData from a inp.xml file can be extracted.'
)
fleurinpd = FleurinpData(files=[filename])
if not fleurinp or dry_run:
structure = fleurinpd.get_structuredata_ncf()
else:
structure = fleurinpd.get_structuredata()
formula = structure.get_formula()
if dry_run:
echo.echo_success(f'parsed structure with formula {formula}')
else:
structure.store()
echo.echo_success(
f'parsed and stored StructureData<{structure.pk}> with formula {formula}, also stored FleurinpData<{fleurinpd.pk}>'
)
def get_results_relax(self):
"""
Generates results of the workchain.
Creates a new structure data node which is an
optimized structure.
"""
if self.ctx.wf_dict.get('relaxation_type', 'atoms') is None:
input_scf = AttributeDict(
self.exposed_inputs(FleurScfWorkChain, namespace='scf'))
if 'structure' in input_scf:
structure = input_scf.structure
elif 'fleurinp' in input_scf:
structure = input_scf.fleurinp.get_structuredata_ncf()
else:
pass
self.ctx.final_structure = structure
self.ctx.final_cell = structure.cell
# The others are already put to None
return
try:
relax_out = self.ctx.scf_res.outputs.last_fleur_calc_output
last_fleur = find_nested_process(self.ctx.scf_res, FleurCalc)[-1]
retrieved_node = last_fleur.outputs.retrieved
except NotExistent:
return self.exit_codes.ERROR_NO_SCF_OUTPUT
relax_out = relax_out.get_dict()
try:
total_energy = relax_out['energy']
total_energy_units = relax_out['energy_units']
atomtype_info = relax_out['relax_atomtype_info']
except KeyError:
return self.exit_codes.ERROR_NO_RELAX_OUTPUT
self.ctx.total_energy_last = total_energy
self.ctx.total_energy_units = total_energy_units
self.ctx.atomtype_info = atomtype_info
fleurinp = FleurinpData(files=['inp.xml', 'relax.xml'],
node=retrieved_node)
structure = fleurinp.get_structuredata_ncf()
self.ctx.final_structure = structure
# -*- coding: utf-8 -*-
"""Helper for regenerating inp.xml files
"""
from aiida import load_profile
load_profile()
from aiida.orm import load_node
from aiida.engine import run
from aiida.plugins import CalculationFactory
from aiida_fleur.data.fleurinp import FleurinpData
inpgenc = CalculationFactory('fleur.inpgen')
path = './inp.xml'
fleurinp = FleurinpData(inpxml=path)
struc = fleurinp.get_structuredata_ncf()
param = fleurinp.get_parameterdata_ncf()
inpgen_code = load_node()
runa = run(inpgenc, code=inpgen_code, structure=struc, calc_parameter=param)