def test_ethanol_basic(self):
"""
Check basic bond parser is working for example of ethanol.
"""
parsed_bonds = parse_bonds(open(self.calc1_path + ".castep").read()).next()
# Make sure we parse all the bonds
self.assertEqual(len(parsed_bonds), 32)
def load_bonds(self, castep_file, pop_tol=0.2):
from castepy.output.bonds import parse_bonds
from collections import Counter
bonds = parse_bonds(castep_file)
bonded_dict = {(atom.species,atom.index): [] for atom in self}
for idx1, idx2, pop, length in bonds:
if pop >= pop_tol:
bonded_dict[idx1].append(idx2)
bonded_dict[idx2].append(idx1)
for idx1, idx2s in bonded_dict.items():
atom1 = self.get_species(*idx1)
bonded_atoms = []
for idx2 in idx2s:
atom2 = self.get_species(*idx2)
bonded_atoms.append(atom2)
atom1.bonded = MagresAtomsView(list(bonded_atoms), self.lattice)
def load_bonds(self, castep_file, pop_tol=0.2):
from castepy.output.bonds import parse_bonds
from collections import Counter
bonds = next(parse_bonds(castep_file))
bonded_dict = dict([((atom.species, atom.index), []) for atom in self])
for idx1, idx2, pop, length in bonds:
if pop >= pop_tol:
bonded_dict[idx1].append(idx2)
bonded_dict[idx2].append(idx1)
for idx1, idx2s in list(bonded_dict.items()):
atom1 = self.get(*idx1)
bonded_atoms = []
for idx2 in idx2s:
atom2 = self.get(*idx2)
bonded_atoms.append(atom2)
atom1.bonded = MagresAtomsView(list(bonded_atoms), self.lattice)
