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_system_nucsize():
#create some atoms
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [2, 2, 2])
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
#test that atoms are set properly
assert len(sys.get_allatoms()) == 16
#now calculate nucsize
sys.set_nucsize_parameters(0.867, 6, 0.5, 0.5)
#sys.calculate_nucsize()
assert sys.calculate_nucsize() == 16
#check the atom cluster props
atoms = sys.get_allatoms()
atom = atoms[0]
cluster = atom.get_cluster()
assert atom.get_cluster() == [1,0,1,1]
assert sys.get_largestcluster() == 1
#assert np.round(sys.get_connection(atoms[0], atoms[1]), decimals=2) == 1.00
#nothing to assert - just check if it works
sys.calculate_frenkelnumbers()
sys.find_clusters()
assert sys.find_largest_cluster() == 16
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_system_atom_access():
#create some atoms
atoms, boxdims = pcs.make_crystal('bcc')
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
atom = sys.get_atom(0)
assert atom.get_x() == [0, 0, 0]
atom.set_x([0.1, 0.1, 0.1])
sys.set_atom(atom)
atom = sys.get_atom(0)
assert atom.get_x() == [0.1, 0.1, 0.1]
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_create_multislice_dump():
"""
Create a multitest dump file and test it
"""
atoms, boxdims = pcs.make_crystal('bcc', repetitions=[6, 6, 6])
sys = pc.System()
sys.assign_atoms(atoms, boxdims)
ptp.write_structure(sys, "tests/bcc1.dump")
atoms2, boxdims2 = pcs.make_crystal('bcc', repetitions=[6, 6, 6])
#modify the coordinates of one atom
x = atoms2[0].get_x()
x[0] += 0.01
atoms2[0].set_x(x)
#write it out
sys2 = pc.System()
sys2.assign_atoms(atoms2, boxdims2)
ptp.write_structure(sys2, "tests/bcc2.dump")
#now merge the two dump files
os.system("cat tests/bcc1.dump tests/bcc2.dump > tests/bcc3.dat")
os.remove("tests/bcc1.dump")
os.remove("tests/bcc2.dump")
#now this file should have info of both - read it in
sys3 = pc.System()
sys3.read_inputfile("tests/bcc3.dat", frame=1)
atoms = sys3.get_allatoms()
assert atoms[0].get_x() == [0.01, 0, 0]
#now this file should have info of both - read it in
sys4 = pc.System()
sys4.read_inputfile("tests/bcc3.dat", frame=0)
atoms = sys4.get_allatoms()
assert atoms[0].get_x() == [0.0, 0, 0]
#now cleanup
os.remove("tests/bcc3.dat")
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_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]
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
def test_basic_system():
#basic system tests
sys = pc.System()
