def test_lammps_dump():
sys = pc.System()
sys.read_inputfile('tests/conf.dump')
atoms = sys.get_allatoms()
assert len(atoms) == 500
#check box
assert sys.get_box() == [[-7.66608, 11.1901],[-7.66915, 11.1931],[-7.74357, 11.2676]]
#check few atoms
filtered_atoms = [ atom for atom in atoms if atom.get_id() == 204]
assert filtered_atoms[0].get_x() == [-0.10301, -6.35752, -6.44787]
#now check the same for zipped file
sys = pc.System()
sys.read_inputfile('tests/conf.dump.gz')
atoms = sys.get_allatoms()
assert len(atoms) == 500
#check box
assert sys.get_box() == [[-7.66608, 11.1901],[-7.66915, 11.1931],[-7.74357, 11.2676]]
#check few atoms
filtered_atoms = [ atom for atom in atoms if atom.get_id() == 204]
assert filtered_atoms[0].get_x() == [-0.10301, -6.35752, -6.44787]
def test_csm_ovito():
sys = pc.System()
sys.read_inputfile("tests/bcc.csm.dump", customkeys=["Centrosymmetry"])
sys.calculate_centrosymmetry(nmax=8)
atoms = sys.atoms
ind = np.random.randint(0, len(atoms))
assert np.abs(atoms[ind].centrosymmetry -
float(atoms[ind].custom["Centrosymmetry"])) < 1E-5
def test_triclinic():
sys = pc.System()
sys.read_inputfile('tests/conf.primitive.bcc.supercell.dump')
sys.get_neighbors(method = 'cutoff', cutoff=1.2)
atoms = sys.get_allatoms()
neighs = atoms[0].get_neighbors()
assert len(neighs) == 14
sys.get_neighbors(method = 'cutoff', cutoff=0.9)
atoms = sys.get_allatoms()
neighs = atoms[0].get_neighbors()
assert len(neighs) == 8
def test_poscar():
sys = pc.System()
sys.read_inputfile('tests/POSCAR', format='poscar')
atoms = sys.get_allatoms()
assert len(atoms) == 42
#now assert atoms of different types
type1 = len([atom for atom in atoms if atom.get_type() == 1])
type2 = len([atom for atom in atoms if atom.get_type() == 2])
type3 = len([atom for atom in atoms if atom.get_type() == 3])
assert type1 == 38
assert type2 == 2
assert type3 == 2
#now test the coorfinates of the atom
assert sys.get_box() == [[0.0, 18.768662916], [0.0, 8.9728430088], [0.0, 2.83746]]
#now check coordinates of first atom
assert atoms[0].get_x() == [0.020389021322710754, 8.8981229427339, 0.0005978263145216028]