def test_neigh():
conf = Configuration()
fname = "configs_extxyz/bilayer_graphene/bilayer_sep3.36_i0_j0.xyz"
conf.read(fname)
conf.species[0] = "O"
neigh = NeighborList(conf, infl_dist=2, padding_need_neigh=False)
fname = "tmp_test_neighbor.xyz"
cell = conf.get_cell()
PBC = conf.get_PBC()
coords = neigh.get_coords()
species = neigh.get_species()
write_config(fname, cell, PBC, species, coords, fmt="extxyz")
assert np.allclose(coords, target_coords)
assert np.array_equal(species, target_species)
# contributing
for i in range(conf.get_number_of_atoms()):
nei_indices, nei_coords, nei_species = neigh.get_neigh(i)
assert np.allclose(nei_indices, all_indices[i])
# padding
for i in range(conf.get_number_of_atoms(), len(coords)):
nei_indices, nei_coords, nei_species = neigh.get_neigh(i)
assert nei_indices.size == 0
assert nei_coords.size == 0
assert nei_species.size == 0
numneigh, neighlist = neigh.get_numneigh_and_neighlist_1D(
request_padding=False)
np.array_equal(numneigh, all_numneigh)
np.array_equal(neighlist, np.concatenate(all_indices))
def test_configuration(e=True, f=False, s=False, order=False):
fname = "./configs_extxyz/MoS2/MoS2"
if e:
fname += "_energy"
if f:
fname += "_forces"
if s:
fname += "_stress"
fname += ".xyz"
config = Configuration(format="extxyz", order_by_species=order)
config.read(fname)
natoms = config.get_number_of_atoms()
cell = config.get_cell()
PBC = config.get_PBC()
species = config.get_species()
coords = config.get_coordinates()
if e:
energy = config.get_energy()
if f:
forces = config.get_forces()
if s:
stress = config.get_stress()
assert natoms == 288
assert np.allclose(
cell,
[
[33.337151, 0.035285, 0.03087],
[0.027151, 25.621674, -0.000664],
[0.027093, 9e-05, 30.262626],
],
)
assert np.allclose(PBC, [1, 1, 1])
if e:
assert energy == -5.302666
if s:
assert np.allclose(stress, [1.1, 2.2, 3.3, 4.4, 5.5, 6.6])
if order:
ref_species = ["Mo", "Mo", "Mo", "Mo", "Mo", "Mo"]
ref_coords = [
[0.051823, -0.017150, 16.736001],
[2.819495, 1.607633, 16.734550],
[5.601008, 0.015314, 16.738646],
]
ref_forces = [
[-0.425324, 0.295866, -0.065479],
[0.245043, -0.061658, 0.264104],
[-0.164382, -0.103679, -0.050262],
]
else:
ref_species = ["Mo", "Mo", "S", "S", "S", "S"]
ref_coords = [
[0.051823, -0.017150, 16.736001],
[2.819495, 1.607633, 16.734550],
[1.901722, -0.004881, 18.317009],
]
ref_forces = [
[-0.425324, 0.295866, -0.065479],
[0.245043, -0.061658, 0.264104],
[0.010127, 0.041539, 0.301571],
]
assert_1d_array(species[:6], ref_species)
assert np.allclose(coords[:3], ref_coords)
if f:
assert np.allclose(forces[:3], ref_forces)
natoms_by_species = config.count_atoms_by_species()
assert natoms_by_species["Mo"] == 96
assert natoms_by_species["S"] == 192
if not e:
energy = None
if not f:
forces = None
if not s:
stress = None
outname = fname.replace("./configs_extxyz/MoS2/MoS2", "tmp_Mos2")
write_extxyz(outname, cell, PBC, species, coords, energy, forces, stress)