def test_neighbors_system_filter():
#create some atoms
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [2, 2, 2])
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
sys.get_neighbors(method = 'cutoff', cutoff=0.867)
#any atom should have 8 neighbors
atoms = sys.get_allatoms()
assert atoms[0].get_coordination() == 8
#now we take all the neighbors of atom0 and replace half of
#them with a different type
neighs = atoms[0].get_neighbors()
#replace the neighs
atoms[neighs[0]].set_type(2)
atoms[neighs[1]].set_type(2)
#now set these atoms back
#for atom in atoms:
sys.set_atom(atoms[neighs[0]])
sys.set_atom(atoms[neighs[1]])
#recalculate neighbors with filter
sys.get_neighbors(method = 'cutoff', cutoff=0.867, filter='type')
#any atom should have 8 neighbors
atoms = sys.get_allatoms()
assert atoms[0].get_coordination() == 6
def test_q_4():
atoms, boxdims = pcs.make_crystal('bcc', repetitions=[4, 4, 4])
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
#sys.get_neighbors(method = 'voronoi')
sys.get_neighbors(method='cutoff', cutoff=0.9)
sys.calculate_q([4, 6], averaged=True)
atoms = sys.get_allatoms()
assert np.round(atoms[0].get_q(4), decimals=2) == 0.51
assert np.round(atoms[0].get_q(4, averaged=True), decimals=2) == 0.51
assert np.round(atoms[0].get_q([4, 6])[0], decimals=2) == 0.51
assert np.round(atoms[0].get_q([4, 6], averaged=True)[1],
decimals=2) == 0.63
assert np.round(atoms[0].get_q([4, 6]), decimals=2)[0] == 0.51
assert np.round(atoms[0].get_q([4, 6], averaged=True)[1],
decimals=2) == 0.63
#now change the q4 values
atoms[0].set_q(4, .23)
atoms[0].set_q(4, .23, averaged=True)
assert np.round(atoms[0].get_q(4), decimals=2) == 0.23
assert np.round(atoms[0].get_q(4, averaged=True), decimals=2) == 0.23
atoms[0].set_q([4, 6], [.23, .46])
atoms[0].set_q([4, 6], [.23, .46], averaged=True)
assert np.round(atoms[0].get_q(4), decimals=2) == 0.23
assert np.round(atoms[0].get_q(4, averaged=True), decimals=2) == 0.23
assert np.round(atoms[0].get_q(6), decimals=2) == 0.46
assert np.round(atoms[0].get_q(6, averaged=True), decimals=2) == 0.46
def test_q_list():
#this might take a while, it will find all qs
atoms, boxdims = pcs.make_crystal('bcc', repetitions=[4, 4, 4])
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
sys.get_neighbors(method='voronoi')
sys.calculate_q([2, 4], averaged=True)
q = sys.get_qvals([2, 4], averaged=True)
def test_q_8():
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [4, 4, 4])
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
sys.get_neighbors(method = 'voronoi')
sys.calculate_q(8, averaged=True)
q = sys.get_qvals(8, averaged=True)
assert np.round(np.mean(np.array(q)), decimals=2) == 0.33
def test_voro_props():
atoms, boxdims = pcs.make_crystal('bcc', repetitions=[2, 2, 2])
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
sys.get_neighbors(method='voronoi')
atoms = sys.get_allatoms()
atom = atoms[0]
v = atom.get_vorovector()
assert v == [0, 6, 0, 8]
def test_q_4():
atoms, boxdims = pcs.make_crystal('bcc', repetitions=[4, 4, 4])
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
#sys.get_neighbors(method = 'voronoi')
sys.get_neighbors(method='cutoff', cutoff=0.9)
sys.calculate_q(4, averaged=True)
q = sys.get_qvals(4, averaged=True)
assert np.round(np.mean(np.array(q)),
decimals=2) == 0.51, "Calculated q4 value is wrong!"
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_q_2():
#this might take a while, it will find all qs
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [6, 6, 6])
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
#sys.read_inputfile("tests/bcc.dat")
sys.get_neighbors(method = 'voronoi')
#sys.get_neighbors(method = 'cutoff', cutoff=0.9)
sys.calculate_q(2)
q = sys.get_qvals(2)
assert np.round(np.mean(np.array(q)), decimals=2) == 0.00
def test_q_2():
#this might take a while, it will find all qs
atoms, boxdims = pcs.make_crystal('bcc', repetitions=[6, 6, 6])
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
#sys.read_inputfile("tests/bcc.dat")
sys.get_neighbors(method='voronoi')
atoms = sys.get_allatoms()
vols = []
avgvols = []
for atom in atoms:
vols.append(atom.get_volume())
avgvols.append(atom.get_volume(averaged=True))
assert np.mean(np.array(vols)) == 0.5
assert np.mean(np.array(avgvols)) == 0.5
def test_neighbors_system():
#create some atoms
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [6, 6, 6])
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
#test that atoms are set properly
assert len(sys.get_allatoms()) == 432
#then lets find neighbors
#cutoff method - first shell only
sys.get_neighbors(method = 'cutoff', cutoff=0.867)
#any atom should have 8 neighbors
atoms = sys.get_allatoms()
assert atoms[0].get_coordination() == 8
sys.reset_neighbors()
#cutoff method - second shell
sys.get_neighbors(method = 'cutoff', cutoff=1.1)
#any atom should have 8 neighbors
atoms = sys.get_allatoms()
assert atoms[0].get_coordination() == 14
#cutoff method - third shell
sys.get_neighbors(method = 'cutoff', cutoff=1.5)
#any atom should have 8 neighbors
atoms = sys.get_allatoms()
assert atoms[0].get_coordination() == 26
sys.reset_neighbors()
#voronoi method - first shell only
sys.get_neighbors(method = 'voronoi')
#any atom should have 8 neighbors
atoms = sys.get_allatoms()
assert atoms[0].get_coordination() == 14
assert np.round(sys.get_distance(atoms[0], atoms[1]), decimals=2) == 0.87