mirror of https://github.com/phonopy/phono3py.git
236 lines
4.0 KiB
Python
236 lines
4.0 KiB
Python
"""Tests of displacements.py."""
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import phono3py
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import numpy as np
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from phono3py.phonon3.displacement_fc3 import get_smallest_vector_of_atom_pair
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distances_NaCl = [
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0.0000000,
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5.6903015,
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5.6903015,
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8.0473015,
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5.6903015,
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8.0473015,
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8.0473015,
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9.8558913,
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4.0236508,
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6.9691675,
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4.0236508,
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6.9691675,
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4.0236508,
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6.9691675,
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4.0236508,
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6.9691675,
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4.0236508,
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4.0236508,
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6.9691675,
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6.9691675,
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4.0236508,
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4.0236508,
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6.9691675,
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6.9691675,
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4.0236508,
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4.0236508,
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4.0236508,
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4.0236508,
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6.9691675,
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6.9691675,
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6.9691675,
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6.9691675,
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4.9279456,
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4.9279456,
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4.9279456,
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4.9279456,
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4.9279456,
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4.9279456,
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4.9279456,
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4.9279456,
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2.8451507,
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2.8451507,
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6.3619505,
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6.3619505,
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6.3619505,
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6.3619505,
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8.5354522,
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8.5354522,
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2.8451507,
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6.3619505,
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2.8451507,
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6.3619505,
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6.3619505,
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8.5354522,
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6.3619505,
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8.5354522,
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2.8451507,
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6.3619505,
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6.3619505,
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8.5354522,
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2.8451507,
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6.3619505,
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6.3619505,
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8.5354522,
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]
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def test_duplicates_agno2(agno2_cell):
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"""Test duplicated pairs of displacements."""
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ph3 = phono3py.load(unitcell=agno2_cell, supercell_matrix=[1, 1, 1])
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ph3.generate_displacements()
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duplicates_ref = [
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[106, 22],
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[220, 80],
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[252, 81],
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[221, 96],
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[253, 97],
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[290, 142],
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[348, 244],
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[364, 245],
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[349, 276],
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[365, 277],
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[119, 0],
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[261, 0],
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[229, 0],
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[260, 0],
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[228, 0],
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]
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np.testing.assert_equal(duplicates_ref, ph3.dataset["duplicates"])
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def test_nacl_pbe(nacl_pbe):
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"""Test generated displacements and duplicates."""
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ph3 = nacl_pbe
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ph3.generate_displacements()
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duplicates_ref = [[77, 41]]
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ph3.dataset["duplicates"]
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np.testing.assert_equal(duplicates_ref, ph3.dataset["duplicates"])
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pairs_ref = [
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0,
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0,
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0,
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1,
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0,
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2,
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0,
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3,
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0,
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6,
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0,
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7,
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0,
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8,
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0,
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9,
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0,
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16,
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0,
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17,
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0,
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18,
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0,
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19,
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0,
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32,
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0,
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33,
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0,
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40,
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0,
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41,
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0,
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42,
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0,
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43,
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0,
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46,
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0,
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47,
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0,
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48,
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0,
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49,
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0,
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52,
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0,
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53,
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32,
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0,
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32,
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1,
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32,
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8,
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32,
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9,
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32,
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10,
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32,
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11,
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32,
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14,
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32,
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15,
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32,
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16,
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32,
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17,
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32,
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20,
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32,
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21,
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32,
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32,
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32,
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33,
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32,
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34,
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32,
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35,
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32,
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38,
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32,
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39,
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32,
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40,
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32,
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41,
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32,
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48,
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32,
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49,
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32,
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50,
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32,
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51,
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]
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pairs = []
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for first_atoms in ph3.dataset["first_atoms"]:
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n1 = first_atoms["number"]
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n2s = np.unique(
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[second_atoms["number"] for second_atoms in first_atoms["second_atoms"]]
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)
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pairs += [[n1, n2] for n2 in n2s]
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# print("".join(["%d, " % i for i in np.array(pairs).ravel()]))
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np.testing.assert_equal(pairs_ref, np.array(pairs).ravel())
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def test_get_smallest_vector_of_atom_pair(nacl_pbe):
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"""Test get_smallest_vector_of_atom_pair."""
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ph3 = nacl_pbe
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distances = []
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for i in range(len(ph3.supercell)):
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vec = get_smallest_vector_of_atom_pair(i, 0, ph3.supercell, 1e-5)
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if vec.ndim == 2:
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vec = vec[0]
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distances.append(np.linalg.norm(np.dot(vec, ph3.supercell.cell)))
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# _show(distances)
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np.testing.assert_allclose(distances_NaCl, distances, rtol=0, atol=1e-6)
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def _show(vals):
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for i, v in enumerate(vals):
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print("%.7f, " % v, end="")
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if (i + 1) % 5 == 0:
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print("")
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