def test_cna_adaptive():
atoms, box = pcs.make_crystal(structure="fcc",
repetitions=(7, 7, 7),
lattice_constant=4.00,
noise=0.1)
sys = pc.System()
sys.atoms = atoms
sys.box = box
sys.calculate_cna(cutoff=None)
atoms = sys.atoms
assert atoms[0].structure == 1
atoms, box = pcs.make_crystal(structure="hcp",
repetitions=(7, 7, 7),
lattice_constant=4.00,
noise=0.1)
sys = pc.System()
sys.atoms = atoms
sys.box = box
sys.calculate_cna(cutoff=None)
atoms = sys.atoms
assert atoms[0].structure == 2
atoms, box = pcs.make_crystal(structure="bcc",
repetitions=(7, 7, 7),
lattice_constant=4.00,
noise=0.1)
sys = pc.System()
sys.atoms = atoms
sys.box = box
sys.calculate_cna(cutoff=None)
atoms = sys.atoms
assert atoms[0].structure == 3
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.box = boxdims
sys.atoms = atoms
ptp.write_file(sys, "tests/bcc1.dump")
atoms2, boxdims2 = pcs.make_crystal('bcc', repetitions=[6, 6, 6])
#modify the coordinates of one atom
x = atoms2[0].pos
x[0] += 0.01
atoms2[0].pos = x
assert len(atoms2) == 432
#write it out
sys2 = pc.System()
sys2.box = boxdims2
sys2.atoms = atoms2
ptp.write_file(sys2, "tests/bcc2.dump")
#now cleanup
if os.path.exists("tests/bcc1.dat"):
os.remove("tests/bcc1.dat")
if os.path.exists("tests/bcc2.dat"):
os.remove("tests/bcc2.dat")
def return_possible_polys(struct):
if struct=='bcc':
atoms, box = pcs.make_crystal('bcc', lattice_constant=4, repetitions=[3,3,3])
sys = pc.System()
sys.atoms = atoms
sys.box = box
sys.find_neighbors(method='voronoi')
sys.calculate_vorovector()
voros = [" ".join(np.array(atom.vorovector).astype(str)) for atom in sys.atoms]
#take unique
unique_voros = np.unique(voros)
elif struct=='fcc':
atoms, box = pcs.make_crystal('fcc', lattice_constant=4, repetitions=[3,3,3])
sys = pc.System()
sys.atoms = atoms
sys.box = box
sys.find_neighbors(method='voronoi')
sys.calculate_vorovector()
voros = [" ".join(np.array(atom.vorovector).astype(str)) for atom in sys.atoms]
#take unique
unique_voros = np.unique(voros)
elif struct=='liquid':
sys = pc.System()
sys.read_inputfile('datafiles/lqd.dat')
sys.find_neighbors(method='voronoi')
sys.calculate_vorovector()
voros = [" ".join(np.array(atom.vorovector).astype(str)) for atom in sys.atoms]
#take unique
unique_voros = np.unique(voros)
elif struct=='distorted-bcc':
sys = pc.System()
sys.read_inputfile('datafiles/mixed_bcc.dat')
sys.find_neighbors(method='voronoi')
sys.calculate_vorovector(edge_cutoff=0.0, area_cutoff=0.0)
voros = [" ".join(np.array(atom.vorovector).astype(str)) for atom in sys.atoms if atom.vorovector[1] >= 2]
#take unique
unique_voros = np.unique(voros)
elif struct=='distorted-fcc':
sys = pc.System()
sys.read_inputfile('datafiles/mixed_fcc.dat')
sys.find_neighbors(method='voronoi')
sys.calculate_vorovector()
voros = [" ".join(np.array(atom.vorovector).astype(str)) for atom in sys.atoms]
#take unique
unique_voros = np.unique(voros)
#now create a dropdown widget with this option
poly_widget = widgets.Dropdown(
options=unique_voros,
value=unique_voros[0],
description='polyhedra:',
disabled=False,
)
return widgets.interact(visualise_poly, poly=poly_widget, atoms=widgets.fixed(sys.atoms))
def test_neighbors_system_filter():
#create some atoms
atoms, boxdims = pcs.make_crystal('bcc', repetitions=[2, 2, 2])
sys = pc.System()
sys.atoms = atoms
sys.box = boxdims
sys.find_neighbors(method='cutoff', cutoff=0.867)
#any atom should have 8 neighbors
atoms = sys.atoms
assert atoms[0].coordination == 8
#now we take all the neighbors of atom0 and replace half of
#them with a different type
neighs = atoms[0].neighbors
#replace the neighs
atoms[neighs[0]].type = 2
atoms[neighs[1]].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.find_neighbors(method='cutoff', cutoff=0.867, filter='type')
#any atom should have 8 neighbors
atoms = sys.atoms
assert atoms[0].coordination == 6
def test_q_4():
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [4, 4, 4])
sys = pc.System()
sys.atoms = atoms
sys.box = boxdims
#sys.get_neighbors(method = 'voronoi')
sys.find_neighbors(method = 'cutoff', cutoff=0.9)
sys.calculate_q([4, 6], averaged=True)
atoms = sys.atoms
#assert np.round(atoms[0].q[2], 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_file_system():
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [1, 1, 1])
sys = pc.System()
sys.atoms = atoms
sys.box = boxdims
sys.find_neighbors(method = 'voronoi')
sys.to_file('tests/tjkf.dat')
#now try to read in the file
sys2 = pc.System()
sys2.read_inputfile('tests/tjkf.dat')
assert len(sys2.atoms) == 2
#now add some custom values
atoms[0].custom = {"velocity":12}
atoms[1].custom = {"velocity":24}
#now try to read in the file
sys3 = pc.System()
sys3.atoms = atoms
sys3.box = boxdims
sys3.to_file('tests/tjkf.dat', custom=['velocity'])
#now read it again
sys4 = pc.System()
sys4.read_inputfile('tests/tjkf.dat', customkeys=['velocity'])
#now get atoms and check them
atoms = sys4.atoms
assert int(atoms[0].custom['velocity']) == 12
assert int(atoms[1].custom['velocity']) == 24
def test_create_structure():
structure = ['bcc', 'fcc', 'hcp', 'diamond', 'a15', 'l12', 'b2']
natoms = [2, 4, 4, 8, 8, 4, 2]
for count, struct in enumerate(structure):
#dumpfile = os.path.join(os.getcwd(), "test.dat")
atoms, boxdims = pcs.make_crystal(struct)
assert len(atoms) == natoms[count]
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.atoms = atoms
sys.box = 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].pos
x[0] += 0.01
atoms2[0].pos = x
assert len(atoms2) == 432
#write it out
sys2 = pc.System()
sys2.atoms = atoms2
sys2.box = 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.atoms
assert len(atoms) == 432
assert atoms[0].pos == [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.atoms
assert atoms[0].pos == [0.0, 0, 0]
#now cleanup
os.remove("tests/bcc3.dat")
def test_rdf():
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [4, 4, 4])
sys = pc.System()
sys.atoms = atoms
sys.box = boxdims
rdf, r = sys.calculate_rdf()
args = np.argsort(rdf)
assert(np.round(r[args][-1], decimals=2) == 0.87)
#test for an fcc type
atoms, boxdims = pcs.make_crystal('fcc', repetitions = [4, 4, 4])
sys = pc.System()
sys.atoms = atoms
sys.box = boxdims
rdf, r = sys.calculate_rdf()
args = np.argsort(rdf)
assert(np.round(r[args][-1], decimals=2) == 0.69)
def test_cna_cutoff():
atoms, box = pcs.make_crystal(structure="fcc",
repetitions=(7, 7, 7),
lattice_constant=4.00,
noise=0.01)
sys = pc.System()
sys.atoms = atoms
sys.box = box
vec = sys.calculate_cna(cutoff=0.8536 * 4.1)
assert vec[1] == 7 * 7 * 7 * 4
def test_voro_props():
atoms, boxdims = pcs.make_crystal('bcc', repetitions=[10, 10, 10])
sys = pc.System()
sys.box = boxdims
sys.atoms = atoms
sys.find_neighbors(method='voronoi')
sys.calculate_vorovector()
atoms = sys.atoms
atom = atoms[0]
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.atoms = atoms
sys.box = boxdims
sys.find_neighbors(method='voronoi')
sys.calculate_q([2, 4], averaged=True)
q = sys.get_qvals([2, 4], averaged=True)
def test_q_10():
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [4, 4, 4])
sys = pc.System()
sys.atoms = atoms
sys.box = boxdims
sys.find_neighbors(method = 'voronoi')
sys.calculate_q(10, averaged=True)
q = sys.get_qvals(10, averaged=True)
assert np.round(np.mean(np.array(q)), decimals=2) == 0.41
def test_cutoff():
atoms, box = pcs.make_crystal(structure="fcc",
lattice_constant=4.07,
repetitions=(6, 6, 6))
sys = pc.System()
sys.box = box
sys.atoms = atoms
sys.find_neighbors(method="cutoff", cutoff=0)
sys.set_atom_cutoff(factor=2)
atoms = sys.atoms
assert (atoms[0].cutoff - 5.755849198858498) < 1E-5
def test_q_4():
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [4, 4, 4])
sys = pc.System()
sys.atoms = atoms
sys.box = boxdims
#sys.get_neighbors(method = 'voronoi')
sys.find_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_angular():
atoms, boxdims = pcs.make_crystal('diamond', repetitions=[4, 4, 4])
sys = pc.System()
sys.atoms = atoms
sys.box = boxdims
sys.find_neighbors(method='voronoi')
sys.calculate_angularcriteria()
q = [atom.angular for atom in sys.atoms]
assert np.round(np.mean(np.array(q)), decimals=2) == 0.00
def test_chiparamsbcc():
atoms, box = pcs.make_crystal('bcc',
repetitions=[3, 3, 3],
lattice_constant=4)
sys = pc.System()
sys.box = box
sys.atoms = atoms
sys.find_neighbors(method='cutoff', cutoff=0)
sys.calculate_chiparams()
atoms = sys.atoms
chip = atoms[2].chiparams
assert chip == [3, 0, 0, 0, 36, 12, 0, 36, 0]
def test_q_access():
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [4, 4, 4])
sys = pc.System()
sys.atoms = atoms
sys.box = boxdims
#sys.get_neighbors(method = 'voronoi')
sys.find_neighbors(method = 'cutoff', cutoff=0.9)
sys.calculate_q([4, 6], averaged=True)
atoms = sys.atoms
assert np.round(sys.get_custom(atoms[1], ["aq4"]), decimals=2)[0] == 0.51
assert np.round(sys.get_custom(atoms[1], ["q4"]), decimals=2)[0] == 0.51
def test_system_nucsize_fraction():
#create some atoms
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [2, 2, 2], lattice_constant=3.20)
sys = pc.System()
sys.box = boxdims
sys.atoms = atoms
#test that atoms are set properly
assert len(sys.atoms) == 16
#now calculate nucsize
sys.find_neighbors(method='cutoff', cutoff=3.63)
assert 16 == sys.find_solids(bonds=0.8, threshold=0.5, avgthreshold=0.6, cluster=True)
def test_neighbors_adaptive():
#create some atoms
atoms, boxdims = pcs.make_crystal('bcc', repetitions = [6, 6, 6])
sys = pc.System()
sys.box = boxdims
sys.atoms = atoms
#then lets find neighbors
#SANN algo test
sys.find_neighbors(method = 'cutoff', cutoff='adaptive')
#any atom should have 8 neighbors
atoms = sys.atoms
assert atoms[0].coordination == 14
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.atoms = atoms
sys.box = boxdims
#sys.read_inputfile("tests/bcc.dat")
sys.find_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_6_voro():
atoms, boxdims = pcs.make_crystal('fcc', repetitions = [4, 4, 4])
sys = pc.System()
sys.atoms = atoms
sys.box = boxdims
sys.find_neighbors(method = 'voronoi')
sys.calculate_q(6)
q = sys.get_qvals(6)
assert np.round(np.mean(np.array(q)), decimals=2) == 0.57 , "Calculated q4 value is wrong!"
sys.calculate_q(6, only_averaged=True)
q = sys.get_qvals(6, averaged=True)
assert np.round(np.mean(np.array(q)), decimals=2) == 0.57 , "Calculated q4 value is wrong!"
def test_neighbors_diamond():
atoms, box = pcs.make_crystal(structure="diamond",
lattice_constant=5.67,
repetitions=(6, 6, 6))
sys = pc.System()
sys.box = box
sys.atoms = atoms
sys.find_diamond_neighbors()
sys.calculate_q([4, 6], averaged=True)
assert (np.mean(sys.get_qvals(4)) - 0.19094065395649326) < 1E-2
assert (np.mean(sys.get_qvals(6)) - 0.5745242597140696) < 1E-2
atoms, box = pcs.make_crystal(structure="fcc",
lattice_constant=4.07,
repetitions=(6, 6, 6))
sys = pc.System()
sys.box = box
sys.atoms = atoms
sys.find_neighbors(method="cutoff", cutoff=0)
sys.calculate_q([4, 6], averaged=True)
assert (np.mean(sys.get_qvals(4)) - 0.19094065395649326) < 1E-2
assert (np.mean(sys.get_qvals(6)) - 0.5745242597140696) < 1E-2
atoms, box = pcs.make_crystal(structure="fcc",
lattice_constant=4.07,
repetitions=(6, 6, 6))
sys = pc.System()
sys.box = box
sys.atoms = atoms
sys.find_diamond_neighbors()
sys.calculate_q([4, 6], averaged=True)
assert (np.mean(sys.get_qvals(4)) - 0.210287193019979) < 1E-2
assert (np.mean(sys.get_qvals(6)) - 0.2350776015575979) < 1E-2
def test_q4_condition():
atoms, boxdims = pcs.make_crystal('l12', repetitions = [8, 8, 8])
sys = pc.System()
sys.box = boxdims
sys.atoms = atoms
sys.find_neighbors(method = 'cutoff', cutoff=0.9)
sys.find_solids()
sys.calculate_q(4, condition="solid")
q = sys.get_qvals(4)
assert np.round(np.mean(np.array(q)), decimals=2) == 0.19 , "Calculated q4 value is wrong!"
sys.calculate_q(4, clear_condition=True, only_averaged=True)
q = sys.get_qvals(4, averaged=True)
assert np.round(np.mean(np.array(q)), decimals=2) == 0.19 , "Calculated q4 value is wrong!"
def test_file_system():
atoms, boxdims = pcs.make_crystal('bcc', repetitions=[1, 1, 1])
sys = pc.System()
sys.box = boxdims
sys.atoms = atoms
sys.find_neighbors(method='voronoi')
sys.to_file('tests/tjkf.dat')
#now try to read in the file
sys2 = pc.System()
sys2.read_inputfile('tests/tjkf.dat')
assert len(sys2.atoms) == 2
#now add some custom values
atoms[0].custom = {"velocity": 12}
atoms[1].custom = {"velocity": 24}
#now try to read in the file
sys3 = pc.System()
sys3.box = boxdims
sys3.atoms = atoms
sys3.to_file('tests/tjkf.dat', customkeys=['velocity'])
#now read it again
sys4 = pc.System()
sys4.read_inputfile('tests/tjkf.dat', customkeys=['velocity'])
#now get atoms and check them
atoms = sys4.atoms
assert int(atoms[0].custom['velocity']) == 12
assert int(atoms[1].custom['velocity']) == 24
sys4.to_file('tests/tjkf.dat.gz', customkeys=['velocity'], compressed=True)
#now read it again
sys5 = pc.System()
sys5.read_inputfile('tests/tjkf.dat.gz', customkeys=['velocity'])
#now get atoms and check them
atoms = sys5.atoms
assert int(atoms[0].custom['velocity']) == 12
assert int(atoms[1].custom['velocity']) == 24
sys6 = pc.System()
sys6.read_inputfile('tests/tjkf.dat')
sys6.to_file('tests/poscar_1', format="poscar", species=['Mo'])
sys6.to_file('tests/data_1', format="lammps-data", species=['Mo'])
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.atoms = atoms
sys.box = boxdims
#sys.read_inputfile("tests/bcc.dat")
sys.find_neighbors(method='voronoi')
atoms = sys.atoms
vols = []
avgvols = []
for atom in atoms:
vols.append(atom.volume)
avgvols.append(atom.avg_volume)
assert np.mean(np.array(vols)) == 0.5
assert np.mean(np.array(avgvols)) == 0.5
def test_system_atom_access():
#create some atoms
atoms, boxdims = pcs.make_crystal('bcc')
sys = pc.System()
sys.box = boxdims
sys.atoms = atoms
#fetch an atom
xoxo = sys.get_atom(0)
assert xoxo.pos == [0, 0, 0]
#change pos pf ayom
xoxo.pos = [1.1, 2.1, 3.1]
sys.set_atom(xoxo)
atom = sys.get_atom(0)
assert atom.pos == [1.1, 2.1, 3.1]
def test_neighbors_number():
atoms, box = pcs.make_crystal(structure="fcc",
repetitions=(3, 3, 3),
lattice_constant=4.00)
sys = pc.System()
sys.box = box
sys.atoms = atoms
sys.find_neighbors(method="number", nmax=8)
atoms = sys.atoms
nns = np.mean([atom.coordination for atom in atoms])
assert nns == 8
sys.find_neighbors(method="number", nmax=12)
atoms = sys.atoms
nns = np.mean([atom.coordination for atom in atoms])
assert nns == 12
def test_cs_ges():
atoms, boxdims = pcs.make_crystal('bcc',
repetitions=[4, 4, 4],
lattice_constant=4.00)
sys = pc.System()
sys.box = boxdims
sys.atoms = atoms
sys.calculate_centrosymmetry(nmax=8)
atoms = sys.atoms
q = [atom.centrosymmetry for atom in atoms]
assert np.round(np.mean(np.array(q)), decimals=2) == 0.00
sys.calculate_centrosymmetry(nmax=12)
atoms = sys.atoms
q = [atom.centrosymmetry for atom in atoms]
assert np.round(np.mean(np.array(q)), decimals=2) > 0.00
def test_sro():
atoms, box = pcs.make_crystal('l12', lattice_constant=4.00, repetitions=[2,2,2])
sys = pc.System()
sys.box = box
sys.atoms = atoms
sys.find_neighbors(method='cutoff', cutoff=4.5)
sro = sys.calculate_sro(reference_type=1, average=True)
assert np.round(sro[0], decimals=2) == -0.33
assert sro[1] == 1.0
atoms = sys.atoms
sro = atoms[4].sro
assert np.round(sro[0], decimals=2) == -0.33
assert sro[1] == 1.0
sys.find_neighbors(method='cutoff', cutoff=4.5)
sro = sys.calculate_sro(reference_type=1, average=True, shells=1)
assert np.round(sro[0], decimals=2) == 0.11
