How to use the pyscal.core function in pyscal

def test_system_nucsize_fraction():
    #create some atoms
    atoms, boxdims = pcs.make_crystal('bcc', repetitions = [2, 2, 2])
    sys = pc.System()
    sys.atoms = atoms
    sys.box = boxdims

    #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_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

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_chiparamsbcc():
    atoms, box = pcs.make_crystal('bcc', repetitions=[3,3,3], lattice_constant=4)
    sys = pc.System()
    sys.atoms = atoms
    sys.box = box
    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_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

def test_chiparamsdia():
    atoms, box = pcs.make_crystal('diamond', repetitions=[3,3,3], lattice_constant=4)
    sys = pc.System()
    sys.atoms = atoms
    sys.box = box
    sys.find_neighbors(method='cutoff', cutoff=0)
    sys.calculate_chiparams()
    atoms = sys.atoms
    chip = atoms[2].chiparams
    assert chip ==  [0, 0, 0, 0, 6, 0, 0, 0, 0]

def test_system_nucsize():
    #create some atoms
    atoms, boxdims = pcs.make_crystal('bcc', repetitions = [2, 2, 2])
    sys = pc.System()
    sys.atoms = atoms
    sys.box = boxdims

    #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=6, threshold=0.5, avgthreshold=0.6, cluster=True)

    #check the atom cluster props
    #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()

def test_basic_system():
    #basic system tests
    sys = pc.System()
    #sys.set_box([[0,1],[0,1],[0,1]])

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)

def test_q_4_size():
    atoms, boxdims = pcs.make_crystal('bcc', repetitions = [5, 5, 6])
    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!"