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# fmt: off
import numpy as np
import pytest
import ase
import ase.lattice.hexagonal
from ase.build import bulk, molecule
from ase.neighborlist import (
first_neighbors,
mic,
neighbor_list,
primitive_neighbor_list,
)
@pytest.mark.slow()
def test_neighbor_kernel():
tol = 1e-7
# two atoms
a = ase.Atoms('CC', positions=[[0.5, 0.5, 0.5], [1, 1, 1]],
cell=[10, 10, 10],
pbc=True)
i, j, d = neighbor_list("ijd", a, 1.1)
assert (i == np.array([0, 1])).all()
assert (j == np.array([1, 0])).all()
assert np.abs(d - np.array([np.sqrt(3 / 4), np.sqrt(3 / 4)])).max() < tol
rng = np.random.RandomState(42)
# test_neighbor_list
for pbc in [True, False, [True, False, True]]:
a = ase.Atoms('4001C', cell=[29, 29, 29])
a.set_scaled_positions(rng.random((len(a), 3)))
j, dr, i, abs_dr, shift = neighbor_list("jDidS", a, 1.85)
assert (np.bincount(i) == np.bincount(j)).all()
r = a.get_positions()
dr_direct = mic(r[j] - r[i], a.cell)
assert np.abs(r[j] - r[i] + shift.dot(a.cell) - dr_direct).max() < tol
abs_dr_from_dr = np.sqrt(np.sum(dr * dr, axis=1))
abs_dr_direct = np.sqrt(np.sum(dr_direct * dr_direct, axis=1))
assert np.all(np.abs(abs_dr - abs_dr_from_dr) < 1e-12)
assert np.all(np.abs(abs_dr - abs_dr_direct) < 1e-12)
assert np.all(np.abs(dr - dr_direct) < 1e-12)
# test_neighbor_list_atoms_outside_box
for pbc in [True, False, [True, False, True]]:
a = ase.Atoms('4001C', cell=[29, 29, 29])
a.set_scaled_positions(rng.random((len(a), 3)))
a.set_pbc(pbc)
a.positions[100, :] += a.cell[0, :]
a.positions[200, :] += a.cell[1, :]
a.positions[300, :] += a.cell[2, :]
j, dr, i, abs_dr, shift = neighbor_list("jDidS", a, 1.85)
assert (np.bincount(i) == np.bincount(j)).all()
r = a.get_positions()
dr_direct = mic(r[j] - r[i], a.cell)
assert np.abs(r[j] - r[i] + shift.dot(a.cell) - dr_direct).max() < tol
abs_dr_from_dr = np.sqrt(np.sum(dr * dr, axis=1))
abs_dr_direct = np.sqrt(np.sum(dr_direct * dr_direct, axis=1))
assert np.all(np.abs(abs_dr - abs_dr_from_dr) < 1e-12)
assert np.all(np.abs(abs_dr - abs_dr_direct) < 1e-12)
assert np.all(np.abs(dr - dr_direct) < 1e-12)
# test_small_cell
a = ase.Atoms('C', positions=[[0.5, 0.5, 0.5]], cell=[1, 1, 1],
pbc=True)
i, j, dr, shift = neighbor_list("ijDS", a, 1.1)
assert np.bincount(i)[0] == 6
assert (dr == shift).all()
i, j = neighbor_list("ij", a, 1.5)
assert np.bincount(i)[0] == 18
a.set_pbc(False)
i = neighbor_list("i", a, 1.1)
assert len(i) == 0
a.set_pbc([True, False, False])
i = neighbor_list("i", a, 1.1)
assert np.bincount(i)[0] == 2
a.set_pbc([True, False, True])
i = neighbor_list("i", a, 1.1)
assert np.bincount(i)[0] == 4
# test_out_of_cell_small_cell
a = ase.Atoms('CC', positions=[[0.5, 0.5, 0.5],
[1.1, 0.5, 0.5]],
cell=[1, 1, 1], pbc=False)
i1, j1, r1 = neighbor_list("ijd", a, 1.1)
a.set_cell([2, 1, 1])
i2, j2, r2 = neighbor_list("ijd", a, 1.1)
assert (i1 == i2).all()
assert (j1 == j2).all()
assert np.abs(r1 - r2).max() < tol
# test_out_of_cell_large_cell
a = ase.Atoms('CC', positions=[[9.5, 0.5, 0.5],
[10.1, 0.5, 0.5]],
cell=[10, 10, 10], pbc=False)
i1, j1, r1 = neighbor_list("ijd", a, 1.1)
a.set_cell([20, 10, 10])
i2, j2, r2 = neighbor_list("ijd", a, 1.1)
assert (i1 == i2).all()
assert (j1 == j2).all()
assert np.abs(r1 - r2).max() < tol
# test_hexagonal_cell
for sx in range(3):
a = ase.lattice.hexagonal.Graphite('C', latticeconstant=(2.5, 10.0),
size=[sx + 1, sx + 1, 1])
i = neighbor_list("i", a, 1.85)
assert np.all(np.bincount(i) == 3)
# test_first_neighbors
i = [1, 1, 1, 1, 3, 3, 3]
assert (first_neighbors(5, i) == np.array([0, 0, 4, 4, 7, 7])).all()
i = [0, 1, 2, 3, 4, 5]
assert (first_neighbors(6, i) == np.array([0, 1, 2, 3, 4, 5, 6])).all()
# test_multiple_elements
a = molecule('HCOOH')
a.center(vacuum=5.0)
i = neighbor_list("i", a, 1.85)
assert (np.bincount(i) == np.array([2, 3, 1, 1, 1])).all()
cutoffs = {(1, 6): 1.2}
i = neighbor_list("i", a, cutoffs)
assert (np.bincount(i) == np.array([0, 1, 0, 0, 1])).all()
cutoffs = {(6, 8): 1.4}
i = neighbor_list("i", a, cutoffs)
assert (np.bincount(i) == np.array([1, 2, 1])).all()
cutoffs = {('H', 'C'): 1.2, (6, 8): 1.4}
i = neighbor_list("i", a, cutoffs)
assert (np.bincount(i) == np.array([1, 3, 1, 0, 1])).all()
cutoffs = [0.0, 0.9, 0.0, 0.5, 0.5]
i = neighbor_list("i", a, cutoffs)
assert (np.bincount(i) == np.array([0, 1, 0, 0, 1])).all()
cutoffs = [0.7, 0.9, 0.7, 0.5, 0.5]
i = neighbor_list("i", a, cutoffs)
assert (np.bincount(i) == np.array([2, 3, 1, 1, 1])).all()
# test_noncubic
a = bulk("Al", cubic=False)
i, j, d = neighbor_list("ijd", a, 3.1)
assert (np.bincount(i) == np.array([12])).all()
assert np.abs(d - [2.86378246] * 12).max() < tol
# test pbc
nat = 10
atoms = ase.Atoms(numbers=range(nat),
cell=[(0.2, 1.2, 1.4),
(1.4, 0.1, 1.6),
(1.3, 2.0, -0.1)])
atoms.set_scaled_positions(3 * rng.random((nat, 3)) - 1)
for p1 in range(2):
for p2 in range(2):
for p3 in range(2):
atoms.set_pbc((p1, p2, p3))
i, j, d, D, S = neighbor_list(
"ijdDS", atoms, atoms.numbers * 0.2 + 0.5)
c = np.bincount(i, minlength=len(atoms))
atoms2 = atoms.repeat((p1 + 1, p2 + 1, p3 + 1))
i2, j2, d2, _D2, _S2 = neighbor_list(
"ijdDS", atoms2, atoms2.numbers * 0.2 + 0.5)
c2 = np.bincount(i2, minlength=len(atoms))
c2.shape = (-1, nat)
dd = d.sum() * (p1 + 1) * (p2 + 1) * (p3 + 1) - d2.sum()
pos = atoms.positions
dr = np.linalg.solve(
atoms.cell.T, (pos[1] - pos[0]).T).T + np.array([0, 0, 3])
assert abs(dd) < 1e-10
assert not (c2 - c).any()
c = 0.0058
i, j, d = primitive_neighbor_list('ijd',
[True, True, True],
np.eye(3) * 7.56,
np.array([[0, 0, 0],
[0, 0, 0.99875]]),
[c, c],
self_interaction=False,
use_scaled_positions=True)
assert np.all(i == [0, 1])
assert np.all(j == [1, 0])
assert np.allclose(d, [0.00945, 0.00945])
# Empty atoms object
i, D, d, j, S = neighbor_list("iDdjS", ase.Atoms(), 1.0)
assert i.dtype == int
assert j.dtype == int
assert d.dtype == float
assert D.dtype == float
assert S.dtype == int
assert i.shape == (0,)
assert j.shape == (0,)
assert d.shape == (0,)
assert D.shape == (0, 3)
assert S.shape == (0, 3)
# Check that only a scalar (not a tuple) is returned if we request a single
# argument.
i = neighbor_list("i", ase.Atoms(), 1.0)
assert i.dtype == int
assert i.shape == (0,)
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