from ...potential_definitions import PotSectionDefinition, \
PotValueDefinition
from ...potential_sections import PotentialSection as PotSection, RepeatedPotentialSection
from ....common.grammar_types import NumpyArray, RawData
from ....common.unique_values import UniqueValuesMapping
from ....common.warnings import DataValidityWarning
from ....common.configuration_definitions import SeparatorDefinition
import re
[docs]class ChargeSection(PotSection):
pass
[docs]class ChargesSection(RepeatedPotentialSection):
[docs] def _set_from_atoms(self, atoms, write_io_data):
self.clear()
if not write_io_data.has_converged_data(self._container):
return
for site, i in write_io_data.sites.unique_items():
charge = self.add(i)
charge.TYPE = i
charge.DATA = site.charge.raw_value
[docs] def _update_atoms(self, atoms, read_io_data):
if len(self):
try:
for site, id in UniqueValuesMapping.from_values(atoms.sites).unique_items():
site.charge = self[id - 1]['DATA']()
except KeyError:
DataValidityWarning("There is no CHARGE data for the atom type with id {id}.")
[docs] def _depends_on(self):
return 'TYPES'
[docs]class ChargeSectionDefinition(PotSectionDefinition):
[docs] def __init__(self, name='CHARGE', **kwargs):
V = PotValueDefinition
members = [
V('TYPE', int),
V('DATA', NumpyArray(line_length=100, shape=(2,-1), ends_with=re.compile("\n(={79}|-{79})"),
ends_with_str = "=" * 79, item_format='% .14E', indented=1),
name_in_grammar=False,
),
V('FULLPOT', RawData(ends_with=re.compile("\n?={79}"), ends_with_str="=" * 79, condition=lambda x: len(x)), required=False,
name_in_grammar=False, write_condition = lambda x: x() != ''),
SeparatorDefinition('=', length=79)
]
super().__init__(name, members, has_hidden_members=True, is_repeated=True, is_optional=True)
result_class = ChargeSection
repeated_class = ChargesSection
section = ChargeSectionDefinition