def test_d2_at_Z(self):
lattice = np.array([[5.29, 0.0, 0.0], [0.0, 15.0, 0.0],
[-0.756071, 0.0, 5.237142]])
positions = np.array([[0.286607, 0.490220, 0.435572],
[0.414891, 0.496366, 0.780603],
[0.546188, 0.504194, 0.217210],
[0.681347, 0.501510, 0.598678],
[0.090962, 0.507718, 0.704071],
[0.182893, 0.512417, 0.074836],
[0.823989, 0.511788, 0.925624],
[0.899757, 0.501391, 0.302911]])
numbers = np.array([4, 4, 4, 4, 6, 6, 6, 6])
modcell = ModifiedCell(lattice, positions, numbers)
modcell.d2_at_Z(z=15.0)
expect_lattice = np.array([[5.29, 0.0,
0.0], [-0.756071, 5.237142, 0.0],
[0.0, 0.0, 15.0]])
expect_positions = np.array([[0.286607, 0.435572, 0.490220],
[0.414891, 0.780603, 0.496366],
[0.546188, 0.217210, 0.504194],
[0.681347, 0.598678, 0.501510],
[0.090962, 0.704071, 0.507718],
[0.182893, 0.074836, 0.512417],
[0.823989, 0.925624, 0.511788],
[0.899757, 0.302911, 0.501391]])
expect_numbers = np.array([4, 4, 4, 4, 6, 6, 6, 6])
self.assertTrue(np.array_equal(modcell.lattice, expect_lattice))
self.assertTrue(np.array_equal(modcell.positions, expect_positions))
self.assertTrue(np.array_equal(modcell.numbers, expect_numbers))
def setUp(self):
self.latt = np.array([[12., 2., 14.], [16., 0., 16.], [2., 2., 0.]])
self.pos = np.array([[0.0, 0.0, 0.0], [0.0, 0.125, 0.0],
[0.0, 0.25, 0.0], [0.0, 0.375, 0.0],
[0.0, 0.5, 0.0], [0.0, 0.625, 0.0],
[0.0, 0.75, 0.0], [0.0, 0.875, 0.0],
[0.25, 0.09375, 0.25], [0.25, 0.21875, 0.25],
[0.25, 0.34375, 0.25], [0.25, 0.46875, 0.25],
[0.25, 0.59375, 0.25], [0.25, 0.71875, 0.25],
[0.25, -0.15625, 0.25], [0.25, -0.03125, 0.25]])
self.numbers = np.array(
[30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 16, 16, 16, 16, 16, 16])
self.initstru = ModifiedCell(self.latt)
self.full_initzb = ModifiedCell(self.latt, self.pos, self.numbers)
def __init__(self, infile, radius):
gcell = GeneralIO.from_file(infile)
self.infile = infile
self.basefname = os.path.basename(infile)
self.mcell = ModifiedCell.from_gcell(gcell)
self.radius = radius
def __init__(self, infile, cenele, radius, ele, refined):
gcell = GeneralIO.from_file(infile)
self.infile = infile
self.basefname = os.path.basename(infile)
self.mcell = ModifiedCell.from_gcell(gcell)
self.clarifier = VerboseAtomRemoveClarifier(Specie(cenele), radius,
Specie(ele))
self.refined = refined
def test_clarify(self):
expect_pos = np.array([[0.208333, 0.333333, 0.375000],
[0.375000, 0.000000, 0.875000],
[0.541667, 0.666667, 0.375000],
[0.708333, 0.333333, 0.875000],
[0.875000, 0.000000, 0.375000],
[0.041667, 0.666667, 0.875000]])
expect_numbers = np.array([16, 16, 16, 16, 55, 55])
expect_newcell = ModifiedCell(self.latt, expect_pos, expect_numbers)
newcell = self.nearZnClarifier.clarify(self.modcell)
self.assertEqual(newcell, expect_newcell)
def test_swap_axis(self):
lattice = np.array([[3.464, 3.0, 0.0], [2.0, 5.99, 0.0],
[0.0, 0.0, 15]])
positions = np.array([[0.014542, 0.690903, 0.508516],
[0.019469, 0.360318, 0.506407],
[0.004450, 0.027941, 0.507198],
[0.464436, 0.525638, 0.502271],
[0.523634, 0.136503, 0.501554],
[0.540583, 0.822100, 0.508352]])
numbers = np.array([4, 4, 6, 6, 6, 6])
modcell = ModifiedCell(lattice, positions, numbers)
modcell.swap_axis((0, 2, 1))
expect_lattice = np.array([[3.464, 0.0, 3.0], [0.0, 15, 0.0],
[2.0, 0.0, 5.99]])
expect_positions = np.array([[0.014542, 0.508516, 0.690903],
[0.019469, 0.506407, 0.360318],
[0.004450, 0.507198, 0.027941],
[0.464436, 0.502271, 0.525638],
[0.523634, 0.501554, 0.136503],
[0.540583, 0.508352, 0.822100]])
expect_numbers = np.array([4, 4, 6, 6, 6, 6])
self.assertTrue(np.array_equal(modcell.lattice, expect_lattice))
self.assertTrue(np.array_equal(modcell.positions, expect_positions))
self.assertTrue(np.array_equal(modcell.numbers, expect_numbers))
def run(self):
import tempfile
working_path = os.getcwd()
for infile in self.files:
basefname = os.path.basename(infile)
# read
gcell = GeneralIO.from_file(infile)
mcell = ModifiedCell.from_gcell(gcell)
new_mcell = self.clarifier.clarify(mcell)
gcell = new_mcell.to_gcell()
# todo: add feature- to convcell.
if self.refined:
gcell = gcell.get_refined_pcell()
out = GeneralIO(gcell)
ofname = "{:}_ACLR.vasp".format(basefname.split('.')[0])
print("PROCESSING: {:}".format(infile))
out.write_file(ofname)
def test_get_points_in_sphere(self):
latt = np.array([[4.898979, 0.000000, 0.000000],
[2.449490, 4.242641, 0.000000],
[1.632993, -0.000000, 4.618802]])
pos = np.array([[0.208333, 0.333333, 0.375000],
[0.375000, 0.000000, 0.875000],
[0.541667, 0.666667, 0.375000],
[0.708333, 0.333333, 0.875000],
[0.875000, 0.000000, 0.375000],
[0.000000, 0.000000, 0.000000],
[0.166667, 0.666667, 0.500000],
[0.333333, 0.333333, 0.000000],
[0.500000, 0.000000, 0.500000],
[0.666667, 0.666667, 0.000000],
[0.833333, 0.333333, 0.500000],
[0.041667, 0.666667, 0.875000]])
numbers = np.array([16, 16, 16, 16, 16, 30, 30, 30, 30, 30, 30, 55])
modcell = ModifiedCell(latt, pos, numbers)
dict_sites = modcell.get_points_incell_insphere(
np.array([0.041667, 0.666667, 0.875000]), 2)
sites = [
Site(pos[5], 'Zn'),
Site(pos[9], 'Zn'),
Site(pos[7], 'Zn'),
Site(pos[6], 'Zn'),
Site(pos[11], 'Cs')
]
self.assertEqual(len(dict_sites), 5)
for s in dict_sites.values():
self.assertTrue(s in sites)
# Test for find giving element
modcell = ModifiedCell(latt, pos, numbers)
dict_sites = modcell.get_points_incell_insphere(
np.array([0.041667, 0.666667, 0.875000]), 2, Specie('Zn'))
sites = [
Site(pos[5], 'Zn'),
Site(pos[9], 'Zn'),
Site(pos[7], 'Zn'),
Site(pos[6], 'Zn')
]
self.assertEqual(len(dict_sites), 4)
for s in dict_sites.values():
self.assertTrue(s in sites)
def perturb(files, radius, outmode, verbose):
from ababe.io.io import GeneralIO
from ababe.stru.scaffold import ModifiedCell
from ababe.stru.element import Specie
import os
for infile in files:
basefname = os.path.basename(infile)
# read
gcell = GeneralIO.from_file(infile)
# process
mcell = ModifiedCell.from_gcell(gcell)
mcell.perturb(radius)
# write
out = GeneralIO(mcell.to_gcell())
if outmode == 'stdio':
out.write_file(fname=None, fmt='vasp')
else:
if verbose: print("PROCESSING: {:}".format(infile))
ofname = "{:}_PURB.{:}".format(basefname.split('.')[0], outmode)
out.write_file(ofname)
def setUp(self):
self.latt = np.array([[4.898979, 0.000000, 0.000000],
[2.449490, 4.242641, 0.000000],
[1.632993, -0.000000, 4.618802]])
self.pos = np.array([[0.208333, 0.333333, 0.375000],
[0.375000, 0.000000, 0.875000],
[0.541667, 0.666667, 0.375000],
[0.708333, 0.333333, 0.875000],
[0.875000, 0.000000, 0.375000],
[0.000000, 0.000000, 0.000000],
[0.166667, 0.666667, 0.500000],
[0.333333, 0.333333, 0.000000],
[0.500000, 0.000000, 0.500000],
[0.666667, 0.666667, 0.000000],
[0.833333, 0.333333, 0.500000],
[0.041667, 0.666667, 0.875000]])
self.numbers = np.array(
[16, 16, 16, 16, 55, 30, 30, 30, 30, 30, 30, 55])
self.modcell = ModifiedCell(self.latt, self.pos, self.numbers)
ele = Specie('Zn')
r = 2
self.nearZnClarifier = VerboseAtomRemoveClarifier(
Specie('Cs'), r, Specie('Zn'))
def test_from_to_gcell(self):
gcell = GeneralCell(self.latt, self.pos, self.numbers)
modcell = ModifiedCell.from_gcell(gcell)
new_gcell = modcell.to_gcell()
self.assertTrue(np.allclose(new_gcell.positions, gcell.positions))
class testModifiedCell(unittest.TestCase):
def setUp(self):
self.latt = np.array([[12., 2., 14.], [16., 0., 16.], [2., 2., 0.]])
self.pos = np.array([[0.0, 0.0, 0.0], [0.0, 0.125, 0.0],
[0.0, 0.25, 0.0], [0.0, 0.375, 0.0],
[0.0, 0.5, 0.0], [0.0, 0.625, 0.0],
[0.0, 0.75, 0.0], [0.0, 0.875, 0.0],
[0.25, 0.09375, 0.25], [0.25, 0.21875, 0.25],
[0.25, 0.34375, 0.25], [0.25, 0.46875, 0.25],
[0.25, 0.59375, 0.25], [0.25, 0.71875, 0.25],
[0.25, -0.15625, 0.25], [0.25, -0.03125, 0.25]])
self.numbers = np.array(
[30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 16, 16, 16, 16, 16, 16])
self.initstru = ModifiedCell(self.latt)
self.full_initzb = ModifiedCell(self.latt, self.pos, self.numbers)
def test_from_to_gcell(self):
gcell = GeneralCell(self.latt, self.pos, self.numbers)
modcell = ModifiedCell.from_gcell(gcell)
new_gcell = modcell.to_gcell()
self.assertTrue(np.allclose(new_gcell.positions, gcell.positions))
def test_get_cartesian_from_frac(self):
expect_coor = np.array([[0., 0., 0.], [2., 0., 2.], [4., 0., 4.],
[6., 0., 6.], [8., 0., 8.], [10., 0., 10.],
[12., 0., 12.], [14., 0., 14.], [5., 1., 5.],
[7., 1., 7.], [9., 1., 9.], [11., 1., 11.],
[13., 1., 13.], [15., 1., 15.], [1., 1., 1.],
[3., 1., 3.]])
cart_coor = self.full_initzb.get_cartesian_from_frac(self.pos)
self.assertTrue(np.allclose(cart_coor, expect_coor))
def test_get_frac_from_cart(self):
"""
change a to b and then b to a
make sure that a equals a
"""
expect_coor = self.pos
cart_coor = self.full_initzb.get_cartesian_from_frac(self.pos)
frac_coor = self.full_initzb.get_frac_from_cart(cart_coor)
self.assertTrue(np.allclose(frac_coor, expect_coor))
def test_translate_sites(self):
def get_rand_vec():
# deals with zero vectors.
vector = np.random.randn(3)
vnorm = np.linalg.norm(vector)
return vector / vnorm * 0.2 if vnorm != 0 else get_rand_vec()
stru = self.full_initzb.copy()
stru.translate_sites(0, get_rand_vec())
gcell = stru.to_gcell()
# This is a runabal passive test TODO!!!!
self.assertFalse(np.array_equal(gcell.positions, self.pos))
def test_perturb(self):
stru = self.full_initzb.copy()
stru.perturb(0.1)
gcell = stru.to_gcell()
# This is a runabal passive test TODO!!!!
self.assertFalse(np.array_equal(gcell.positions, self.pos))
stru = self.full_initzb.copy()
stru.perturb(0.0)
gcell = stru.to_gcell()
# This is a runabal passive test TODO!!!!
self.assertTrue(np.array_equal(gcell.positions, self.pos))
def test_swap_axis(self):
lattice = np.array([[3.464, 3.0, 0.0], [2.0, 5.99, 0.0],
[0.0, 0.0, 15]])
positions = np.array([[0.014542, 0.690903, 0.508516],
[0.019469, 0.360318, 0.506407],
[0.004450, 0.027941, 0.507198],
[0.464436, 0.525638, 0.502271],
[0.523634, 0.136503, 0.501554],
[0.540583, 0.822100, 0.508352]])
numbers = np.array([4, 4, 6, 6, 6, 6])
modcell = ModifiedCell(lattice, positions, numbers)
modcell.swap_axis((0, 2, 1))
expect_lattice = np.array([[3.464, 0.0, 3.0], [0.0, 15, 0.0],
[2.0, 0.0, 5.99]])
expect_positions = np.array([[0.014542, 0.508516, 0.690903],
[0.019469, 0.506407, 0.360318],
[0.004450, 0.507198, 0.027941],
[0.464436, 0.502271, 0.525638],
[0.523634, 0.501554, 0.136503],
[0.540583, 0.508352, 0.822100]])
expect_numbers = np.array([4, 4, 6, 6, 6, 6])
self.assertTrue(np.array_equal(modcell.lattice, expect_lattice))
self.assertTrue(np.array_equal(modcell.positions, expect_positions))
self.assertTrue(np.array_equal(modcell.numbers, expect_numbers))
# lattice = np.array([[3.464, 3.0, 0.0],
# [2.0, 5.99, 0.0],
# [0.0, 0.0, 15]])
# positions = np.array([[0.014542, 0.690903, 0.508516],
# [0.019469, 0.360318, 0.506407],
# [0.004450, 0.027941, 0.507198],
# [0.464436, 0.525638, 0.502271],
# [0.523634, 0.136503, 0.501554],
# [0.540583, 0.822100, 0.508352]])
# numbers = np.array([4,4,6,6,6,6])
# modcell = ModifiedCell(lattice, positions, numbers)
# modcell.swap_axis((2,0,1))
# expect_lattice = np.array([[0.0, 0.0, 15],
# [3.464, 3.0, 0.0],
# [2.0, 5.99, 0.0]])
# expect_positions = np.array([[0.508516, 0.014542, 0.690903],
# [0.506407, 0.019469, 0.360318],
# [0.507198, 0.004450, 0.027941],
# [0.502271, 0.464436, 0.525638],
# [0.501554, 0.523634, 0.136503],
# [0.508352, 0.540583, 0.822100]])
# expect_numbers = np.array([4,4,6,6,6,6])
# self.assertTrue(np.array_equal(modcell.lattice, expect_lattice))
# self.assertTrue(np.array_equal(modcell.positions, expect_positions))
# self.assertTrue(np.array_equal(modcell.numbers, expect_numbers))
def test_d2_at_Z(self):
lattice = np.array([[5.29, 0.0, 0.0], [0.0, 15.0, 0.0],
[-0.756071, 0.0, 5.237142]])
positions = np.array([[0.286607, 0.490220, 0.435572],
[0.414891, 0.496366, 0.780603],
[0.546188, 0.504194, 0.217210],
[0.681347, 0.501510, 0.598678],
[0.090962, 0.507718, 0.704071],
[0.182893, 0.512417, 0.074836],
[0.823989, 0.511788, 0.925624],
[0.899757, 0.501391, 0.302911]])
numbers = np.array([4, 4, 4, 4, 6, 6, 6, 6])
modcell = ModifiedCell(lattice, positions, numbers)
modcell.d2_at_Z(z=15.0)
expect_lattice = np.array([[5.29, 0.0,
0.0], [-0.756071, 5.237142, 0.0],
[0.0, 0.0, 15.0]])
expect_positions = np.array([[0.286607, 0.435572, 0.490220],
[0.414891, 0.780603, 0.496366],
[0.546188, 0.217210, 0.504194],
[0.681347, 0.598678, 0.501510],
[0.090962, 0.704071, 0.507718],
[0.182893, 0.074836, 0.512417],
[0.823989, 0.925624, 0.511788],
[0.899757, 0.302911, 0.501391]])
expect_numbers = np.array([4, 4, 4, 4, 6, 6, 6, 6])
self.assertTrue(np.array_equal(modcell.lattice, expect_lattice))
self.assertTrue(np.array_equal(modcell.positions, expect_positions))
self.assertTrue(np.array_equal(modcell.numbers, expect_numbers))
def test_get_points_in_sphere(self):
latt = np.array([[4.898979, 0.000000, 0.000000],
[2.449490, 4.242641, 0.000000],
[1.632993, -0.000000, 4.618802]])
pos = np.array([[0.208333, 0.333333, 0.375000],
[0.375000, 0.000000, 0.875000],
[0.541667, 0.666667, 0.375000],
[0.708333, 0.333333, 0.875000],
[0.875000, 0.000000, 0.375000],
[0.000000, 0.000000, 0.000000],
[0.166667, 0.666667, 0.500000],
[0.333333, 0.333333, 0.000000],
[0.500000, 0.000000, 0.500000],
[0.666667, 0.666667, 0.000000],
[0.833333, 0.333333, 0.500000],
[0.041667, 0.666667, 0.875000]])
numbers = np.array([16, 16, 16, 16, 16, 30, 30, 30, 30, 30, 30, 55])
modcell = ModifiedCell(latt, pos, numbers)
dict_sites = modcell.get_points_incell_insphere(
np.array([0.041667, 0.666667, 0.875000]), 2)
sites = [
Site(pos[5], 'Zn'),
Site(pos[9], 'Zn'),
Site(pos[7], 'Zn'),
Site(pos[6], 'Zn'),
Site(pos[11], 'Cs')
]
self.assertEqual(len(dict_sites), 5)
for s in dict_sites.values():
self.assertTrue(s in sites)
# Test for find giving element
modcell = ModifiedCell(latt, pos, numbers)
dict_sites = modcell.get_points_incell_insphere(
np.array([0.041667, 0.666667, 0.875000]), 2, Specie('Zn'))
sites = [
Site(pos[5], 'Zn'),
Site(pos[9], 'Zn'),
Site(pos[7], 'Zn'),
Site(pos[6], 'Zn')
]
self.assertEqual(len(dict_sites), 4)
for s in dict_sites.values():
self.assertTrue(s in sites)
def test_append(self):
site_s = Site((0, 0, 0.222), 'S')
zb = self.full_initzb.copy()
zb.append(site_s)
gcell = zb.to_gcell()
new_pos = np.insert(self.pos, 1, [[0, 0, 0.222]], axis=0)
new_numbers = np.insert(self.numbers, 1, 16)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
self.assertTrue(np.array_equal(gcell.numbers, new_numbers))
def test_remove_site(self):
stru = self.full_initzb.copy()
new_stru = stru.remove_site()
gcell = new_stru.to_gcell()
new_pos = np.delete(self.pos, 15, 0)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
stru = self.full_initzb.copy()
new_stru = stru.remove_site(2)
gcell = new_stru.to_gcell()
new_pos = np.delete(self.pos, 2, 0)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
def test_append_site(self):
site_s = Site((0, 0, 0.222), 'S')
initstru = self.initstru.copy()
new_stru = initstru.append_site(site_s)
gcell = new_stru.to_gcell()
new_pos = np.append([[0, 0, 0]], [[0, 0, 0.222]], axis=0)
self.assertTrue(new_stru is initstru)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
def test_remove_sites(self):
stru = self.full_initzb.copy()
new_stru = stru.remove_sites([2, 14, 3, 5])
gcell = new_stru.to_gcell()
new_pos = np.delete(self.pos, [2, 14, 3, 5], 0)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
def test_append_sites(self):
l_sites = [Site((0, 0, k), 'S') for k in [0.1, 0.2, 0.3]]
initstru = self.initstru.copy()
new_stru = initstru.append_sites(l_sites)
gcell = new_stru.to_gcell()
new_pos = np.array([[0, 0, 0], [0, 0, 0.1], [0, 0, 0.2], [0, 0, 0.3]])
self.assertTrue(np.array_equal(gcell.positions, new_pos))
def test_copy(self):
new_zb = self.full_initzb.copy()
self.assertEqual(new_zb, self.full_initzb)
self.assertFalse(new_zb is self.full_initzb)
class testModifiedCell(unittest.TestCase):
def setUp(self):
self.latt = np.array([[12., 2., 14.], [16., 0., 16.], [2., 2., 0.]])
self.pos = np.array([[0.0, 0.0, 0.0], [0.0, 0.125, 0.0],
[0.0, 0.25, 0.0], [0.0, 0.375, 0.0],
[0.0, 0.5, 0.0], [0.0, 0.625, 0.0],
[0.0, 0.75, 0.0], [0.0, 0.875, 0.0],
[0.25, 0.09375, 0.25], [0.25, 0.21875, 0.25],
[0.25, 0.34375, 0.25], [0.25, 0.46875, 0.25],
[0.25, 0.59375, 0.25], [0.25, 0.71875, 0.25],
[0.25, -0.15625, 0.25], [0.25, -0.03125, 0.25]])
self.numbers = np.array(
[30, 30, 30, 30, 30, 30, 30, 30, 16, 16, 16, 16, 16, 16, 16, 16])
self.initstru = ModifiedCell(self.latt)
self.full_initzb = ModifiedCell(self.latt, self.pos, self.numbers)
def test_from_to_gcell(self):
gcell = GeneralCell(self.latt, self.pos, self.numbers)
modcell = ModifiedCell.from_gcell(gcell)
new_gcell = modcell.to_gcell()
self.assertTrue(np.allclose(new_gcell.positions, gcell.positions))
def test_get_cartesian_from_frac(self):
expect_coor = np.array([[0., 0., 0.], [2., 0., 2.], [4., 0., 4.],
[6., 0., 6.], [8., 0., 8.], [10., 0., 10.],
[12., 0., 12.], [14., 0., 14.], [5., 1., 5.],
[7., 1., 7.], [9., 1., 9.], [11., 1., 11.],
[13., 1., 13.], [15., 1., 15.], [1., 1., 1.],
[3., 1., 3.]])
cart_coor = self.full_initzb.get_cartesian_from_frac(self.pos)
self.assertTrue(np.allclose(cart_coor, expect_coor))
def test_get_frac_from_cart(self):
"""
change a to b and then b to a
make sure that a equals a
"""
expect_coor = self.pos
cart_coor = self.full_initzb.get_cartesian_from_frac(self.pos)
frac_coor = self.full_initzb.get_frac_from_cart(cart_coor)
self.assertTrue(np.allclose(frac_coor, expect_coor))
def test_translate_sites(self):
def get_rand_vec():
# deals with zero vectors.
vector = np.random.randn(3)
vnorm = np.linalg.norm(vector)
return vector / vnorm * 0.2 if vnorm != 0 else get_rand_vec()
stru = self.full_initzb.copy()
stru.translate_sites(0, get_rand_vec())
gcell = stru.to_gcell()
# This is a runabal passive test TODO!!!!
self.assertFalse(np.array_equal(gcell.positions, self.pos))
def test_perturb(self):
stru = self.full_initzb.copy()
stru.perturb(0.1)
gcell = stru.to_gcell()
# This is a runabal passive test TODO!!!!
self.assertFalse(np.array_equal(gcell.positions, self.pos))
stru = self.full_initzb.copy()
stru.perturb(0.0)
gcell = stru.to_gcell()
# This is a runabal passive test TODO!!!!
self.assertTrue(np.array_equal(gcell.positions, self.pos))
def test_get_points_in_sphere(self):
latt = np.array([[4.898979, 0.000000, 0.000000],
[2.449490, 4.242641, 0.000000],
[1.632993, -0.000000, 4.618802]])
pos = np.array([[0.208333, 0.333333, 0.375000],
[0.375000, 0.000000, 0.875000],
[0.541667, 0.666667, 0.375000],
[0.708333, 0.333333, 0.875000],
[0.875000, 0.000000, 0.375000],
[0.000000, 0.000000, 0.000000],
[0.166667, 0.666667, 0.500000],
[0.333333, 0.333333, 0.000000],
[0.500000, 0.000000, 0.500000],
[0.666667, 0.666667, 0.000000],
[0.833333, 0.333333, 0.500000],
[0.041667, 0.666667, 0.875000]])
numbers = np.array([16, 16, 16, 16, 16, 30, 30, 30, 30, 30, 30, 55])
modcell = ModifiedCell(latt, pos, numbers)
dict_sites = modcell.get_points_incell_insphere(
np.array([0.041667, 0.666667, 0.875000]), 2)
sites = [
Site(pos[5], 'Zn'),
Site(pos[9], 'Zn'),
Site(pos[7], 'Zn'),
Site(pos[6], 'Zn'),
Site(pos[11], 'Cs')
]
self.assertEqual(len(dict_sites), 5)
for s in dict_sites.values():
self.assertTrue(s in sites)
# Test for find giving element
modcell = ModifiedCell(latt, pos, numbers)
dict_sites = modcell.get_points_incell_insphere(
np.array([0.041667, 0.666667, 0.875000]), 2, Specie('Zn'))
sites = [
Site(pos[5], 'Zn'),
Site(pos[9], 'Zn'),
Site(pos[7], 'Zn'),
Site(pos[6], 'Zn')
]
self.assertEqual(len(dict_sites), 4)
for s in dict_sites.values():
self.assertTrue(s in sites)
def test_append(self):
site_s = Site((0, 0, 0.222), 'S')
zb = self.full_initzb.copy()
zb.append(site_s)
gcell = zb.to_gcell()
new_pos = np.insert(self.pos, 1, [[0, 0, 0.222]], axis=0)
new_numbers = np.insert(self.numbers, 1, 16)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
self.assertTrue(np.array_equal(gcell.numbers, new_numbers))
def test_remove_site(self):
stru = self.full_initzb.copy()
new_stru = stru.remove_site()
gcell = new_stru.to_gcell()
new_pos = np.delete(self.pos, 15, 0)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
stru = self.full_initzb.copy()
new_stru = stru.remove_site(2)
gcell = new_stru.to_gcell()
new_pos = np.delete(self.pos, 2, 0)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
def test_append_site(self):
site_s = Site((0, 0, 0.222), 'S')
initstru = self.initstru.copy()
new_stru = initstru.append_site(site_s)
gcell = new_stru.to_gcell()
new_pos = np.append([[0, 0, 0]], [[0, 0, 0.222]], axis=0)
self.assertTrue(new_stru is initstru)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
def test_remove_sites(self):
stru = self.full_initzb.copy()
new_stru = stru.remove_sites([2, 14, 3, 5])
gcell = new_stru.to_gcell()
new_pos = np.delete(self.pos, [2, 14, 3, 5], 0)
self.assertTrue(np.array_equal(gcell.positions, new_pos))
def test_append_sites(self):
l_sites = [Site((0, 0, k), 'S') for k in [0.1, 0.2, 0.3]]
initstru = self.initstru.copy()
new_stru = initstru.append_sites(l_sites)
gcell = new_stru.to_gcell()
new_pos = np.array([[0, 0, 0], [0, 0, 0.1], [0, 0, 0.2], [0, 0, 0.3]])
self.assertTrue(np.array_equal(gcell.positions, new_pos))
def test_copy(self):
new_zb = self.full_initzb.copy()
self.assertEqual(new_zb, self.full_initzb)
self.assertFalse(new_zb is self.full_initzb)