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public distro 2.1.0

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muntwiler_m
2019-07-19 12:54:54 +02:00
parent acea809e4e
commit fbd2d4fa8c
40 changed files with 2813 additions and 345 deletions
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107
tests/test_cluster.py
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@ -10,7 +10,7 @@ to run the tests, change to the directory which contains the tests directory, an
@author Matthias Muntwiler, matthias.muntwiler@psi.ch
@copyright (c) 2015-17 by Paul Scherrer Institut @n
@copyright (c) 2015-19 by Paul Scherrer Institut @n
Licensed under the Apache License, Version 2.0 (the "License"); @n
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
@ -102,16 +102,18 @@ class TestClusterFunctions(unittest.TestCase):
@return: None
"""
clu = self.create_cube()
xy2 = clu.data[['x', 'y']].copy()
xy3 = xy2.view((xy2.dtype[0], len(xy2.dtype.names)))
xy3 = np.empty((clu.data.shape[0], 2), np.float32)
xy3[:, 0] = clu.data['x']
xy3[:, 1] = clu.data['y']
ctr = np.asarray((1.0, 0.0, 0.0))
dist = np.linalg.norm(xy3 - ctr[0:2], axis=1)
self.assertAlmostEqual(1.0, dist[0])
self.assertAlmostEqual(0.0, dist[1])
clu.clear()
xy2 = clu.data[['x', 'y']].copy()
xy3 = xy2.view((xy2.dtype[0], len(xy2.dtype.names)))
xy3 = np.empty((clu.data.shape[0], 2), np.float32)
xy3[:, 0] = clu.data['x']
xy3[:, 1] = clu.data['y']
ctr = np.asarray((1.0, 0.0, 0.0))
dist = np.linalg.norm(xy3 - ctr[0:2], axis=1)
self.assertEqual(0, dist.shape[0])
@ -156,7 +158,7 @@ class TestClusterFunctions(unittest.TestCase):
clu.set_emitter(idx=0)
clu.set_emitter(idx=9)
self.assertEqual(2, clu.get_emitter_count())
result = clu.get_emitters()
result = clu.get_emitters(['x', 'y', 'z', 't'])
expect = [(0., 0., 0., 1), (1., 0., 1., 10)]
self.assertEqual(expect, result)
@ -233,7 +235,7 @@ class TestClusterFunctions(unittest.TestCase):
emitter = np.array((0.0, 0.0, 0.0))
clu.add_layer(7, a1, b1, b2)
pos = clu.find_positions(pos=emitter)
self.assertEqual(len(pos), 1)
self.assertEqual(1, len(pos))
def test_add_cluster(self):
clu1 = mc.Cluster()
@ -244,15 +246,18 @@ class TestClusterFunctions(unittest.TestCase):
clu1.add_atom(5, np.asarray([0, 0, -2]), 0)
clu2 = mc.Cluster()
clu2.add_atom(3, np.asarray([-0.2, 0, 0]), 0)
clu2.add_atom(4, np.asarray([0, -0.2, 0]), 0)
clu2.add_atom(5, np.asarray([0, 0.05, -1]), 0)
clu2.add_atom(5, np.asarray([0, 0, -1.01]), 0)
clu2.add_atom(6, np.asarray([0, 0, -1.99]), 0)
clu2.add_atom(3, np.asarray([-0.2, 0, 0]), 0) # unique
clu2.add_atom(4, np.asarray([0, -0.2, 0]), 0) # unique
clu2.add_atom(5, np.asarray([0, 0.05, -1]), 0) # not unique
clu2.add_atom(5, np.asarray([0, 0, -1.09]), 0) # just within tolerance of uniqueness
clu2.add_atom(6, np.asarray([0, 0, -1.99]), 0) # not unique
clu2.add_atom(7, np.asarray([0, 0, -1.10]), 0) # just out of tolerance of uniqueness
clu1.set_rmax(1.5)
clu1.add_cluster(clu2, check_rmax=True, check_unique=True, tol=0.1)
self.assertEqual(clu1.get_atom_count(), 5+2)
self.assertEqual(5+3, clu1.get_atom_count())
self.assertEqual(7, clu1.data['t'][-1])
self.assertEqual(6, clu2.data.shape[0])
def test_find_positions(self):
clu = mc.Cluster()
@ -269,8 +274,14 @@ class TestClusterFunctions(unittest.TestCase):
clu.add_layer(7, a_N, b1, b2)
clu.add_layer(5, a_B, b1, b2)
pos = clu.find_positions(pos=emitter)
self.assertEqual(len(pos), 1)
self.assertEqual(pos[0], 206)
self.assertEqual(1, len(pos))
self.assertEqual(206, pos[0])
# position in the format returned by get_emitters
emitter = (emitter[0], emitter[1], emitter[2], 7)
pos = clu.find_positions(pos=emitter)
self.assertEqual(1, len(pos))
self.assertEqual(206, pos[0])
def test_find_index_cylinder(self):
clu = self.create_cube()
@ -278,11 +289,11 @@ class TestClusterFunctions(unittest.TestCase):
rxy = 0.5
rz = 1.0
idx = clu.find_index_cylinder(pos, rxy, rz, None)
self.assertEqual(len(idx), 2)
self.assertEqual(clu.get_atomtype(idx[0]), 8)
self.assertEqual(clu.get_atomtype(idx[1]), 20)
self.assertEqual(2, len(idx))
self.assertEqual(8, clu.get_atomtype(idx[0]))
self.assertEqual(20, clu.get_atomtype(idx[1]))
idx = clu.find_index_cylinder(pos, rxy, rz, 8)
self.assertEqual(len(idx), 1)
self.assertEqual(1, len(idx))
def test_trim_cylinder(self):
clu = mc.Cluster()
@ -296,12 +307,12 @@ class TestClusterFunctions(unittest.TestCase):
r0 = 2.3
z0 = 4.2
clu.trim_cylinder(r0, z0)
self.assertEqual(clu.data.dtype, clu.dtype)
self.assertEqual(clu.data.shape[0], 21 * 5)
self.assertEqual(clu.data[1]['i'], 2)
self.assertEqual(clu.data[1]['s'], 'N')
self.assertEqual(clu.data[1]['t'], 7)
self.assertEqual(clu.get_emitter_count(), 1)
self.assertEqual(clu.dtype, clu.data.dtype)
self.assertEqual(21 * 5, clu.data.shape[0])
self.assertEqual(2, clu.data[1]['i'])
self.assertEqual('N', clu.data[1]['s'])
self.assertEqual(7, clu.data[1]['t'])
self.assertEqual(1, clu.get_emitter_count())
n_low = np.sum(clu.data['z'] < -z0)
self.assertEqual(0, n_low)
n_high = np.sum(clu.data['z'] > z0)
@ -320,12 +331,12 @@ class TestClusterFunctions(unittest.TestCase):
clu.set_emitter(pos=v_pos)
r0 = 2.3
clu.trim_sphere(r0)
self.assertEqual(clu.data.dtype, clu.dtype)
self.assertEqual(clu.data.shape[0], 39)
self.assertEqual(clu.data[1]['i'], 2)
self.assertEqual(clu.data[1]['s'], 'N')
self.assertEqual(clu.data[1]['t'], 7)
self.assertEqual(clu.get_emitter_count(), 1)
self.assertEqual(clu.dtype, clu.data.dtype)
self.assertEqual(39, clu.data.shape[0])
self.assertEqual(2, clu.data[1]['i'])
self.assertEqual('N', clu.data[1]['s'])
self.assertEqual(7, clu.data[1]['t'])
self.assertEqual(1, clu.get_emitter_count())
n_out = np.sum(clu.data['x']**2 + clu.data['y']**2 + clu.data['z'] > r0**2)
self.assertEqual(0, n_out)
@ -355,9 +366,9 @@ class TestClusterFunctions(unittest.TestCase):
def test_trim_slab(self):
clu = self.create_cube()
clu.trim_slab('x', 0.5, 1.1)
self.assertEqual(clu.data.dtype, clu.dtype)
self.assertEqual(clu.data.shape[0], 9 * 2)
self.assertEqual(clu.get_emitter_count(), 1)
self.assertEqual(clu.dtype, clu.data.dtype)
self.assertEqual(9 * 2, clu.data.shape[0])
self.assertEqual(1, clu.get_emitter_count())
def test_save_to_file(self):
clu = self.create_cube()
@ -367,12 +378,34 @@ class TestClusterFunctions(unittest.TestCase):
clu.save_to_file(f, mc.FMT_XYZ, "qwerty", emitters_only=True)
f.seek(0)
line = f.readline()
self.assertEqual(line, b"2\n", b"line 1: " + line)
self.assertEqual(b"2\n", line, b"line 1: " + line)
line = f.readline()
self.assertEqual(line, b"qwerty\n", b"line 2: " + line)
self.assertEqual(b"qwerty\n", line, b"line 2: " + line)
line = f.readline()
self.assertRegexpMatches(line, b"H +[0.]+ +[0.]+ +[0.]+", b"line 3: " + line)
line = f.readline()
self.assertRegexpMatches(line, b"Si +[01.-]+ +[01.-]+ +[0.]+", b"line 4: " + line)
line = f.readline()
self.assertEqual(line, b"", b"end of file")
self.assertEqual(b"", line, b"end of file")
def test_update_atoms(self):
clu = mc.Cluster()
clu.add_atom(1, np.asarray([0, 0, 0]), 1)
clu.add_atom(3, np.asarray([0, 1, 0]), 0)
clu.add_atom(5, np.asarray([-1, 0, 0]), 0)
clu.add_atom(6, np.asarray([0, -1, 0]), 0)
clu.add_atom(2, np.asarray([1, 0, 0]), 0)
clu.add_atom(4, np.asarray([0, 0, 1]), 0)
other = mc.Cluster()
other.add_atom(1, np.asarray([0, 0, 0]), 1)
other.add_atom(5, np.asarray([-1, 0, 0]), 0)
other.add_atom(2, np.asarray([1, 0, 0]), 0)
other.add_atom(6, np.asarray([0, -1, 0]), 0)
other.add_atom(3, np.asarray([0, 1, 0]), 0)
other.add_atom(4, np.asarray([0, 0, 1]), 0)
other.data['c'] = np.asarray((1, 2, 2, 3, 3, 4))
clu.update_atoms(other, {'c'})
expected = np.asarray((1, 3, 2, 3, 2, 4))
np.testing.assert_array_equal(expected, clu.data['c'])