def test_list(self):
particle_positions = np.array([[19, -18]])
box_space = np.array([4, 4])
cutoff = 1
s1 = Neighbourlist(particle_positions, box_space, cutoff)
print(s1.calculate_index(np.array([-1, 1])))
print(s1.cell_neighbour_list_2D())
def test_list3d(self):
particle_positions = np.array([[9, 6, 4]])
box_space = np.array([8, 6, 4])
cutoff = 2
s1 = Neighbourlist(particle_positions, box_space, cutoff)
print(s1.calculate_index(np.array([1, 0, 0])))
lol = s1.cell_neighbour_list_3D()
print(lol)
def __init__(self, particles, parameters):
self.particles = particles
self.energy = Energy()
self.k_vectors = [1, 1, 1]
particle_positions = self.get_particle_position_array()
self.neighbourlist = Neighbourlist(particles=particle_positions, Box=parameters.box, rc=parameters.cutoff_radius)
if System.cell_neighbour_list is None:
System.cell_neighbour_list = self.neighbourlist.calc_cell_neighbours()
def test_benchmark(self):
particle_positions = []
for i in range(0, 100000):
xtest = np.random.rand(3)
particle_positions.append(xtest)
particle_positions = np.array(particle_positions)
box_space = np.array([50, 50, 50])
cutoff = 2
s1 = Neighbourlist(particle_positions, box_space, cutoff)
print("rdy")
for i in range(10):
s1.construct_neighbourlist()
print(s1.cell_list)
print(s1.particle_neighbour_list)
def test_cnlist1d_1(self):
particle_positions = np.array([[9], [4], [1]])
box_space = np.array([12])
cutoff = 3
s1 = Neighbourlist(particle_positions, box_space, cutoff)
print(s1.calculate_index(np.array([1, 0, 0])))
reference_CnList = np.array([[3, 0, 1, 2], [0, 1, 2, 3], [1, 2, 3, 0]])
cnlist = s1.cell_neighbour_list_1D()
print(cnlist)
sorted_referenceCnList = np.sort(reference_CnList, axis=0)
sorted_outputCnList = np.sort(cnlist[:, :, 0], axis=0)
npt.assert_equal(sorted_referenceCnList,
sorted_outputCnList,
'Failed',
verbose=True)
class System:
cell_neighbour_list = None
# Test Positions are same dimension
def __init__(self, particles, parameters):
self.particles = particles
self.energy = Energy()
particle_positions = self.get_particle_position_array()
self.neighbourlist = Neighbourlist(particles=particle_positions,
Box=parameters.box,
rc=parameters.cutoff_radius)
if System.cell_neighbour_list is None:
System.cell_neighbour_list = self.neighbourlist.calc_cell_neighbours(
)
def get_particle_position_array(self):
x = []
for i in range(len(self.particles)):
x.append(self.particles[i].position)
y = np.array(x)
return y
def test_1d(self):
particle_positions = np.array([[1], [0], [3], [4], [0]])
box_space = np.array([4])
cutoff = 2
s1 = Neighbourlist(particle_positions, box_space, cutoff)
print(s1.cell_list)
print(s1.particle_neighbour_list)
def test_determine_box_shift(self):
EC = EnergyCalculator(box=np.array([2, 3, 2]),
cutoff_radius=1,
es_sigma=1,
charges=np.array([1]),
lj_sigmas=np.array([1]),
lj_epsilons=np.array([1]),
k_vector=np.array([[1]]))
vector1 = np.array([3, 4, 1])
NL = Neighbourlist(Box=np.array([2, 3, 2]),
particles=np.array([[3, 4, 1]]),
rc=1)
cell_nl = NL.cell_neighbour_list_3D()
EC.cell_neighbour_list = cell_nl
calc_shift = EC._determine_box_shift(0, 2)
reference_shift = np.array([-2, 0, 0])
self.assertTrue(np.array_equal(calc_shift, reference_shift))
def __init__(self, particles, parameters):
self.particles = particles
self.energy = Energy()
self.k_vectors = [1, 1, 1]
x = []
for i in range(len(particles)):
x.append(particles[i].position)
y = np.array(x)
self.neighbourlist = Neighbourlist(particles=y,
Box=parameters.box,
rc=parameters.cutoff_radius)
if System.cell_neighbour_list is None:
System.cell_neighbour_list = self.neighbourlist.calc_cell_neighbours(
)
def test_periodicity(self):
particle_positions = np.array([[19, -18]], dtype=np.int32)
box_space = np.array([2, 2], dtype=np.int32)
cutoff = 1
s1 = Neighbourlist(particle_positions, box_space, cutoff)
print(s1.cell_list)
print(s1.particle_neighbour_list)
def test_3dsecond(self):
particle_positions = np.array([[9, 6, 4], [2.25, 2, 2], [2.3, 4, 1], [9, 4, 2], [0, 0, 0]])
box_space = np.array([9, 6, 4])
cutoff = 2
s1 = Neighbourlist(particle_positions, box_space, cutoff)
print(s1.cell_list)
print(s1.particle_neighbour_list)
def test_3d(self):
particle_positions = np.array([[1, 1, 3], [0, 3, 1], [3, 4, 2], [4, 4, 4], [0, 0, 0]])
box_space = np.array([4, 4, 4])
cutoff = 2
s1 = Neighbourlist(particle_positions, box_space, cutoff)
print(s1.cell_list)
print(s1.particle_neighbour_list)
def test_2dsecond(self):
particle_positions = np.array(
[[0.01, 0.01], [0, 0.03], [0.03, 0.04], [0.05, 0.05], [0.09, 0.09], [0.09, 0], [0.1, 0.1]])
box_space = np.array([0.10, 0.10])
cutoff = 0.025
s1 = Neighbourlist(particle_positions, box_space, cutoff)
print(s1.particle_neighbour_list)
print(s1.cell_list)
def test_string_value(self):
# particle_position_dimension_diff_with_box
particle_positions = np.array([[0.0, 0.5], [1.5, 4.5], [2.5, 2.5],
[3.0, 4.5], [4.5, 5.5], [5.5, 3.5],
[6.0, 5.0], [6.5, 9.5], [7.0, 1.1],
[8.25, 2.0], [9.75, 11.0], ['h', 'm']])
box_space = np.array([10.5, 11.0])
cutoff = 4.6
s1 = Neighbourlist(particle_positions, box_space, cutoff)
def test_2d_output_validation_2(self):
particle_positions = np.array([[13.5, 2.], [14., 5.], [-2., 2.], [25.5, 2.],
[-14., 2.], [13.5, 15.], [-1., -2.]])
box_space = np.array([12., 13.])
cutoff = 3
reference_head = np.asarray([5, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, 4, -1, -1, 6])
reference_neighlist = np.asarray([-1, -1, -1, 0, 2, 3, -1])
s1 = Neighbourlist(particle_positions, box_space, cutoff)
npt.assert_equal(reference_head, s1.cell_list, 'Failed', verbose=True)
npt.assert_equal(reference_neighlist, s1.particle_neighbour_list, 'Failed', verbose=True)
def test_cnlist2d_1(self):
particle_positions = np.array([[9, 6], [4, 5], [1, 3]])
box_space = np.array([12, 13])
cutoff = 3
s1 = Neighbourlist(particle_positions, box_space, cutoff)
reference_CnList = np.array([
[13, 14, 15, 12, 1, 2, 3, 0, 5, 6, 7, 4, 9, 10, 11, 8],
[1, 2, 3, 0, 5, 6, 7, 4, 9, 10, 11, 8, 13, 14, 15, 12],
[5, 6, 7, 4, 9, 10, 11, 8, 13, 14, 15, 12, 1, 2, 3, 0],
[12, 13, 14, 15, 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11],
[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15],
[4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 0, 1, 2, 3],
[15, 12, 13, 14, 3, 0, 1, 2, 7, 4, 5, 6, 11, 8, 9, 10],
[3, 0, 1, 2, 7, 4, 5, 6, 11, 8, 9, 10, 15, 12, 13, 14],
[7, 4, 5, 6, 11, 8, 9, 10, 15, 12, 13, 14, 3, 0, 1, 2]
])
cnlist = s1.cell_neighbour_list_2D()
sorted_referenceCnList = np.sort(reference_CnList, axis=0)
sorted_outputCnList = np.sort(cnlist[:, :, 0], axis=0)
npt.assert_equal(sorted_referenceCnList, sorted_outputCnList, 'Failed', verbose=True)
def test_Bench(self):
particle_positions = []
for i in range(0, 100000):
xtest = np.random.rand(2)
particle_positions.append(xtest)
particle_positions = np.array(particle_positions)
box_space = np.array([1, 1])
cutoff = 0.1
s1 = Neighbourlist(particle_positions, box_space, cutoff)
print(s1.cell_list)
print(s1.particle_neighbour_list)
def test_1d_output_validation_2(self):
particle_positions = np.array([[1.5], [2.5],
[3.0], [4.5], [5.5],
[6.0], [6.5], [7.0],
[8.25], [9.75], [10.0], [11.5], [12.5]])
reference_head = np.asarray([12.0, 6.0, 9.0])
reference_neighlist = np.asarray([-1.0, 0.0, 1.0, -1.0, 3.0, 4.0, 5.0, -1.0, 7.0, 8.0, 2.0, 10.0, 11.0])
box_space = np.array([10])
cutoff = 3
s1 = Neighbourlist(particle_positions, box_space, cutoff)
npt.assert_equal(reference_head, s1.cell_list, 'Failed', verbose=True)
npt.assert_equal(reference_neighlist, s1.particle_neighbour_list, 'Failed', verbose=True)
def test_2d_output_validation_1(self):
particle_positions = np.array([[1.5, 2.], [2, 5.], [2.5, 8.],
[4., 4.], [4., 8.], [5.5, 9.],
[8., 11.], [7., 2.], [6., 5.],
[6., 6.5], [7., 6.5], [10., 2.],
[11., 9.], [11., 11.], [13.5, 2.],
[14., 5.], [-2., 2.], [25.5, 2.],
[-14., 2.], [13.5, 15.], [-1., -2.]])
box_space = np.array([12., 13.])
cutoff = 3
reference_head = np.asarray([19, 15, 2, -1, -1, 3, 5, -1, 7, 8, 10, 6, 18, -1, 12, 20])
reference_neighlist = np.asarray([-1, -1, -1, -1, -1, 4, -1, -1, -1, -1, 9,
-1, -1, -1, 0, 1, 11, 14, 16, 17, 13])
s1 = Neighbourlist(particle_positions, box_space, cutoff)
npt.assert_equal(reference_head, s1.cell_list, 'Failed', verbose=True)
npt.assert_equal(reference_neighlist, s1.particle_neighbour_list, 'Failed', verbose=True)
def test_3d_output_validation(self):
particle_positions = np.array([[1.5, 1., 2.5], [1.5, 4., 2.5], [1.5, 8.5, 2.5],
[1.5, 1., 5.5], [1.5, 4., 5.5], [1.5, 5.5, 5.5],
[1.5, 10., 5.5], [1.5, 1., 8.5], [1.5, 4., 8.5],
[1.5, 8.5, 8.5], [1.5, 4., 11.5], [1.5, 11.5, 11.5],
[4.5, 1., 2.5], [4.5, 5.5, 2.5], [4.5, 7., 2.5],
[4.5, 1., 5.5], [4.5, 4., 5.5], [4.5, 5.5, 5.5],
[4.5, 7., 5.5], [4.5, 10., 5.5], [4.5, 2.5, 8.5],
[4.5, 4., 8.5], [4.5, 5.5, 8.5], [4.5, 8.5, 8.5],
[4.5, 1., 11.5], [4.5, 5.5, 11.5], [7.5, 1., 2.5],
[7.5, 5.5, 2.5], [7.5, 7., 2.5], [7.5, 11.5, 2.5],
[7.5, 1., 5.5], [7.5, 4., 5.5], [7.5, 5.5, 5.5],
[7.5, 10., 5.5], [7.5, 2.5, 8.5], [7.5, 5.5, 8.5],
[7.5, 7., 8.5], [7.5, 11.5, 8.5], [7.5, 4., 11.5],
[7.5, 7., 11.5], [10.5, 1., 2.5], [10.5, 5.5, 2.5],
[10.5, 11.5, 2.5], [10.5, 1., 5.5], [10.5, 2.5, 5.5],
[10.5, 4., 5.5], [10.5, 10., 5.5], [10.5, 11.5, 5.5],
[10.5, 1., 8.5], [10.5, 4., 8.5], [10.5, 11.5, 8.5],
[10.5, 1., 11.5], [10.5, 4., 11.5], [10.5, 11.5, 11.5],
[3., 3.25, 3.5], [6.0, 6.5, 7.0], [6.5, 5.0, 7.0],
[8.0, 6.5, 7.0], [12.0, 6.5, 7.0], [12.0, 6.5, 3.5],
[12.0, 13.0, 7.0], [6.0, 13.0, 7.0], [13.5, 1., 5.5],
[13.5, 4., 5.5], [13.5, 5.5, 5.5], [13.5, 10., 5.5],
[13.5, 14, 5.5], [13.5, 15.5, 5.5], [-1.5, 1., 5.5],
[-1.5, 2.5, 5.5], [-1.5, 4., 5.5], [-1.5, 10., 5.5],
[-1.5, 11.5, 5.5]])
box_space = np.array([12., 13., 14.])
reference_head = np.asarray([0, 67, 60, -1, 1, 64, 8, 10, 2, 59, 58, -1, -1, 65, -1, 11,
12, 15, 20, 24, 13, 54, 22, 25, 14, 18, 23, -1, -1, 19, -1,
- 1, 26, 30, 61, -1, 27, 32, 56, 38, 28, -1, 57, 39, 29, 33,
37, -1, 40, 69, 48, 51, 41, 70, 49, 52, -1, -1, -1, -1, 42,
72, 50, 53])
reference_neighlist = np.asarray([-1, -1, -1, -1, -1, 4, -1, -1, -1, -1, -1, -1, -1, -1,
- 1, -1, -1, 16, -1, -1, -1, -1, 21, -1, -1, -1, -1, -1,
- 1, -1, -1, -1, 31, -1, -1, -1, -1, -1, -1, -1, -1, -1,
- 1, -1, 43, -1, -1, 46, -1, -1, -1, -1, -1, -1, 17, 36,
35, 55, 9, -1, 7, 34, 3, 5, 63, 6, 62, 66, 44, 68, 45,
47, 71, ])
cutoff = 3
s1 = Neighbourlist(particle_positions, box_space, cutoff)
npt.assert_equal(reference_head, s1.cell_list, 'Failed', verbose=True)
npt.assert_equal(reference_neighlist, s1.particle_neighbour_list, 'Failed', verbose=True)
def test_cnlist3d_2(self):
particle_positions = np.array([[9, 6, 4], [4, 5, 6], [1, 3, 6]])
box_space = np.array([12, 10, 10])
cutoff = 3
s1 = Neighbourlist(particle_positions, box_space, cutoff)
reference_CnList = np.array(
[[
31, 32, 30, 34, 35, 33, 28, 29, 27, 4, 5, 3, 7, 8, 6, 1, 2, 0,
13, 14, 12, 16, 17, 15, 10, 11, 9, 22, 23, 21, 25, 26, 24, 19,
20, 18
],
[
4, 5, 3, 7, 8, 6, 1, 2,
0, 13, 14, 12, 16, 17, 15, 10, 11,
9, 22, 23, 21, 25, 26, 24, 19, 20, 18, 31, 32, 30, 34, 35, 33,
28, 29, 27
],
[
13, 14, 12, 16, 17, 15,
10, 11, 9, 22, 23, 21, 25, 26, 24, 19, 20, 18, 31, 32, 30, 34,
35, 33, 28, 29, 27, 4, 5, 3, 7, 8, 6, 1, 2, 0
],
[
28, 29, 27, 31, 32,
30, 34, 35, 33, 1, 2, 0, 4, 5, 3, 7, 8, 6, 10, 11,
9, 13, 14, 12, 16, 17, 15, 19, 20, 18, 22, 23, 21, 25, 26, 24
],
[
1, 2, 0, 4, 5, 3, 7, 8,
6, 10, 11, 9, 13, 14, 12, 16, 17, 15, 19, 20, 18, 22, 23, 21,
25, 26, 24, 28, 29, 27,
31, 32, 30, 34, 35, 33
],
[
10, 11, 9, 13, 14, 12, 16, 17, 15, 19, 20, 18, 22, 23, 21, 25,
26, 24, 28, 29, 27, 31,
32, 30, 34, 35, 33, 1, 2, 0, 4, 5, 3, 7, 8, 6
],
[
34, 35, 33, 28, 29,
27, 31, 32, 30, 7, 8, 6, 1, 2, 0, 4, 5, 3, 16, 17, 15, 10, 11,
9, 13, 14, 12, 25, 26, 24, 19, 20, 18, 22, 23, 21
],
[
7, 8, 6, 1, 2, 0, 4, 5, 3, 16, 17, 15, 10, 11, 9, 13, 14, 12,
25, 26, 24, 19, 20, 18, 22, 23, 21, 34, 35, 33, 28, 29, 27,
31, 32, 30
],
[
16, 17, 15, 10, 11, 9, 13, 14, 12, 25, 26, 24, 19, 20, 18, 22,
23, 21, 34, 35, 33, 28, 29, 27, 31, 32, 30, 7, 8, 6, 1, 2, 0,
4, 5, 3
],
[
30, 31, 32, 33, 34, 35, 27, 28, 29, 3, 4, 5, 6, 7, 8, 0, 1, 2,
12, 13, 14, 15, 16, 17, 9, 10, 11, 21, 22, 23, 24, 25, 26, 18,
19, 20
],
[
3, 4, 5, 6, 7, 8, 0, 1, 2, 12, 13, 14, 15, 16, 17, 9, 10, 11,
21, 22, 23, 24, 25, 26, 18, 19, 20, 30, 31, 32, 33, 34, 35,
27, 28, 29
],
[
12, 13, 14, 15, 16, 17, 9, 10, 11, 21, 22, 23, 24, 25, 26, 18,
19, 20, 30, 31, 32, 33, 34, 35, 27, 28, 29, 3, 4, 5, 6, 7, 8,
0, 1, 2
],
[
27, 28, 29, 30, 31, 32, 33, 34, 35, 0, 1, 2, 3, 4, 5, 6, 7, 8,
9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, 26
],
[
0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17,
18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32,
33, 34, 35
],
[
9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24,
25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 0, 1, 2, 3, 4, 5,
6, 7, 8
],
[
33, 34, 35, 27, 28, 29, 30, 31, 32, 6, 7, 8, 0, 1, 2, 3, 4, 5,
15, 16, 17, 9, 10, 11, 12, 13, 14, 24, 25, 26, 18, 19, 20, 21,
22, 23
],
[
6, 7, 8, 0, 1, 2, 3, 4, 5, 15, 16, 17, 9, 10, 11, 12, 13, 14,
24, 25, 26, 18, 19, 20, 21, 22, 23, 33, 34, 35, 27, 28, 29,
30, 31, 32
],
[
15, 16, 17, 9, 10, 11, 12, 13, 14, 24, 25, 26, 18, 19, 20, 21,
22, 23, 33, 34, 35, 27, 28, 29, 30, 31, 32, 6, 7, 8, 0, 1, 2,
3, 4, 5
],
[
32, 30, 31, 35, 33, 34, 29, 27, 28, 5, 3, 4, 8, 6, 7, 2, 0, 1,
14, 12, 13, 17, 15, 16, 11, 9, 10, 23, 21, 22, 26, 24, 25, 20,
18, 19
],
[
5, 3, 4, 8, 6, 7, 2, 0, 1, 14, 12, 13, 17, 15, 16, 11, 9, 10,
23, 21, 22, 26, 24, 25, 20, 18, 19, 32, 30, 31, 35, 33, 34,
29, 27, 28
],
[
14, 12, 13, 17, 15, 16, 11, 9, 10, 23, 21, 22, 26, 24, 25, 20,
18, 19, 32, 30, 31, 35, 33, 34, 29, 27, 28, 5, 3, 4, 8, 6, 7,
2, 0, 1
],
[
29, 27, 28, 32, 30, 31, 35, 33, 34, 2, 0, 1, 5, 3, 4, 8, 6, 7,
11, 9, 10, 14, 12, 13, 17, 15, 16, 20, 18, 19, 23, 21, 22, 26,
24, 25
],
[
2, 0, 1, 5, 3, 4, 8, 6, 7, 11, 9, 10, 14, 12, 13, 17, 15, 16,
20, 18, 19, 23, 21, 22, 26, 24, 25, 29, 27, 28, 32, 30, 31,
35, 33, 34
],
[
11, 9, 10, 14, 12, 13, 17, 15, 16, 20, 18, 19, 23, 21, 22, 26,
24, 25, 29, 27, 28, 32, 30, 31, 35, 33, 34, 2, 0, 1, 5, 3, 4,
8, 6, 7
],
[
35, 33, 34, 29, 27, 28, 32, 30, 31, 8, 6, 7, 2, 0, 1, 5, 3, 4,
17, 15, 16, 11, 9, 10, 14, 12, 13, 26, 24, 25, 20, 18, 19, 23,
21, 22
],
[
8, 6, 7, 2, 0, 1, 5, 3, 4, 17, 15, 16, 11, 9, 10, 14, 12, 13,
26, 24, 25, 20, 18, 19, 23, 21, 22, 35, 33, 34, 29, 27, 28,
32, 30, 31
],
[
17, 15, 16, 11, 9, 10, 14, 12, 13, 26, 24, 25, 20, 18, 19, 23,
21, 22, 35, 33, 34, 29, 27, 28, 32, 30, 31, 8, 6, 7, 2, 0, 1,
5, 3, 4
]])
cnlist = s1.cell_neighbour_list_3D()
print(cnlist)
sorted_referenceCnList = np.sort(reference_CnList, axis=0)
sorted_outputCnList = np.sort(cnlist[:, :, 0], axis=0)
npt.assert_equal(sorted_referenceCnList,
sorted_outputCnList,
'Failed',
verbose=True)