def read_ion(self, atoms):
"""Read the ion.xml file of each specie
"""
from ase.calculators.siesta.import_ion_xml import get_ion
species, species_numbers = self.species(atoms)
self.results['ion'] = {}
for species_number, spec in enumerate(species):
species_number += 1
if spec['pseudopotential'] is None:
pseudopotential = self.getpath(label, 'psf')
else:
pseudopotential = spec['pseudopotential']
name = os.path.basename(pseudopotential)
name = name.split('.')
if spec['ghost']:
name.insert(-1, 'ghost')
name = '.'.join(name)
label = '.'.join(np.array(name.split('.'))[:-1])
if label not in self.results['ion']:
fname = self.getpath(label, 'ion.xml')
if os.path.isfile(fname):
self.results['ion'][label] = get_ion(fname)
def read_ion(self, atoms):
"""
Read the ion.xml file of each specie
"""
from ase.calculators.siesta.import_ion_xml import get_ion
species, species_numbers = self.species(atoms)
self.results['ion'] = {}
for species_number, spec in enumerate(species):
species_number += 1
symbol = spec['symbol']
atomic_number = atomic_numbers[symbol]
if spec['pseudopotential'] is None:
if self.pseudo_qualifier() == '':
label = symbol
else:
label = '.'.join([symbol, self.pseudo_qualifier()])
pseudopotential = self.getpath(label, 'psf')
else:
pseudopotential = spec['pseudopotential']
label = os.path.basename(pseudopotential)
label = '.'.join(label.split('.')[:-1])
name = os.path.basename(pseudopotential)
name = name.split('.')
name.insert(-1, str(species_number))
if spec['ghost']:
name.insert(-1, 'ghost')
atomic_number = -atomic_number
name = '.'.join(name)
label = '.'.join(np.array(name.split('.'))[:-1])
if label not in self.results['ion']:
fname = self.getpath(label, 'ion.xml')
if os.path.isfile(fname):
self.results['ion'][label] = get_ion(fname)
def read_ion(self, atoms):
"""Read the ion.xml file of each specie
"""
from ase.calculators.siesta.import_ion_xml import get_ion
species, species_numbers = self.species(atoms)
self.results['ion'] = {}
for species_number, specie in enumerate(species):
species_number += 1
symbol = specie['symbol']
atomic_number = atomic_numbers[symbol]
if specie['pseudopotential'] is None:
if self.pseudo_qualifier() == '':
label = symbol
pseudopotential = label + '.psf'
else:
label = '.'.join([symbol, self.pseudo_qualifier()])
pseudopotential = label + '.psf'
else:
pseudopotential = specie['pseudopotential']
label = os.path.basename(pseudopotential)
label = '.'.join(label.split('.')[:-1])
name = os.path.basename(pseudopotential)
name = name.split('.')
name.insert(-1, str(species_number))
if specie['ghost']:
name.insert(-1, 'ghost')
atomic_number = -atomic_number
name = '.'.join(name)
label = '.'.join(np.array(name.split('.'))[:-1])
if label not in self.results['ion']:
fname = label + '.ion.xml'
self.results['ion'][label] = get_ion(fname)