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import pytest
from ase import Atoms
from ase.build import molecule
from ase.symbols import Symbols
@pytest.fixture
def atoms():
return molecule('CH3CH2OH')
@pytest.fixture
def symbols(atoms):
return atoms.symbols
def test_symbols_indexing(atoms):
print(atoms.symbols)
atoms.symbols[0] = 'X'
atoms.symbols[2:4] = 'Pu'
atoms.numbers[6:8] = 79
assert atoms.numbers[0] == 0
assert (atoms.numbers[2:4] == 94).all()
assert sum(atoms.symbols == 'Au') == 2
assert (atoms.symbols[6:8] == 'Au').all()
assert (atoms.symbols[:3] == 'XCPu').all()
print(atoms)
print(atoms.numbers)
def test_symbols_vs_get_chemical_symbols(atoms):
assert atoms.get_chemical_symbols() == list(atoms.symbols)
def test_str_roundtrip(symbols):
string = str(symbols)
newsymbols = Symbols.fromsymbols(string)
assert (symbols == newsymbols).all()
def test_manipulation_with_string():
atoms = molecule('H2O')
atoms.symbols = 'Au2Ag'
print(atoms.symbols)
assert (atoms.symbols == 'Au2Ag').all()
def test_search(atoms):
indices = atoms.symbols.search('H')
assert len(indices) > 0
assert (atoms.symbols[indices] == 'H').all()
assert (atoms[indices].symbols == 'H').all()
def test_search_two(atoms):
indices = atoms.symbols.search('CO')
assert all(sym in {'C', 'O'} for sym in atoms.symbols[indices])
def test_species(atoms):
assert atoms.symbols.species() == set(atoms.symbols)
def test_indices(atoms):
dct = atoms.symbols.indices()
assert set(dct) == atoms.symbols.species()
for symbol, indices in dct.items():
assert all(atoms.symbols[indices] == symbol)
def test_symbols_to_symbols(symbols):
assert all(Symbols(symbols.numbers) == symbols)
def test_symbols_to_atoms(symbols):
assert all(Atoms(symbols).symbols == symbols)
def test_symbols_to_formula():
symstr = 'CH3CH2OH'
symbols = Symbols.fromsymbols(symstr)
assert str(symbols.formula) == symstr
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