def test_k2_weights_and_geoms_finite(self):
"""Tests that the values of the weight and geometry functions are
correct for the k=2 term.
"""
lmbtr = LMBTR(species=[1, 8],
k=[2],
grid=default_grid,
virtual_positions=False,
periodic=False)
lmbtr.create(H2O, positions=[1])
geoms = lmbtr._k2_geoms
weights = lmbtr._k2_weights
# Test against the assumed geom values
pos = H2O.get_positions()
assumed_geoms = {
(0, 1): 2 * [1 / np.linalg.norm(pos[0] - pos[1])],
}
self.dict_comparison(assumed_geoms, geoms)
# Test against the assumed weights
assumed_weights = {
(0, 1): 2 * [1],
}
self.dict_comparison(assumed_weights, weights)
# Test against system with different indexing
lmbtr = LMBTR(species=[1, 8],
k=[2],
grid=default_grid,
virtual_positions=False,
periodic=False)
lmbtr.create(H2O_2, positions=[0])
geoms2 = lmbtr._k2_geoms
self.dict_comparison(geoms, geoms2)
def test_k3_weights_and_geoms_finite(self):
"""Tests that all the correct angles are present in finite systems.
There should be n*(n-1)*(n-2)/2 unique angles where the division by two
gets rid of duplicate angles.
"""
system = Atoms(
scaled_positions=[
[0, 0, 0],
[0.5, 0, 0],
[0, 0.5, 0],
[0.5, 0.5, 0],
],
symbols=["H", "H", "H", "O"],
cell=[10, 10, 10],
pbc=True,
)
lmbtr = LMBTR(species=[1, 8],
k=[3],
grid=default_grid,
virtual_positions=False,
periodic=False)
lmbtr.create(system, positions=[0])
geoms = lmbtr._k3_geoms
weights = lmbtr._k3_weights
# Test against the assumed geom values.
assumed_geoms = {
(0, 1, 1): 2 * [math.cos(45 / 180 * math.pi)],
(0, 2, 1): 2 * [math.cos(45 / 180 * math.pi)],
(0, 1, 2): 2 * [math.cos(90 / 180 * math.pi)],
(1, 0, 2): 2 * [math.cos(45 / 180 * math.pi)],
(1, 0, 1): 1 * [math.cos(90 / 180 * math.pi)],
}
self.dict_comparison(geoms, assumed_geoms)
# Test against the assumed weight values.
assumed_weights = {
(0, 1, 1): 2 * [1],
(0, 2, 1): 2 * [1],
(0, 1, 2): 2 * [1],
(1, 0, 2): 2 * [1],
(1, 0, 1): 1 * [1],
}
self.dict_comparison(weights, assumed_weights)
def test_k2_peaks_finite(self):
"""Tests the correct peak locations and intensities are found for the
k=2 term in finite systems.
"""
desc = LMBTR(
species=["H", "O"],
k2={
"geometry": {
"function": "distance"
},
"grid": {
"min": -1,
"max": 3,
"sigma": 0.5,
"n": 1000
},
"weighting": {
"function": "unity"
},
},
normalize_gaussians=False,
periodic=False,
flatten=True,
sparse=False,
)
features = desc.create(H2O, [0])[0, :]
pos = H2O.get_positions()
x = desc.get_k2_axis()
# Check the X-H peaks
xh_feat = features[desc.get_location(("X", "H"))]
xh_peak_indices = find_peaks(xh_feat, prominence=0.5)[0]
xh_peak_locs = x[xh_peak_indices]
xh_peak_ints = xh_feat[xh_peak_indices]
self.assertTrue(
np.allclose(xh_peak_locs, [np.linalg.norm(pos[0] - pos[2])],
rtol=0,
atol=1e-2))
self.assertTrue(np.allclose(xh_peak_ints, [1], rtol=0, atol=1e-2))
# Check the X-O peaks
xo_feat = features[desc.get_location(("X", "O"))]
xo_peak_indices = find_peaks(xo_feat, prominence=0.5)[0]
xo_peak_locs = x[xo_peak_indices]
xo_peak_ints = xo_feat[xo_peak_indices]
self.assertTrue(
np.allclose(xo_peak_locs,
np.linalg.norm(pos[0] - pos[1]),
rtol=0,
atol=1e-2))
self.assertTrue(np.allclose(xo_peak_ints, [1], rtol=0, atol=1e-2))
# Check that everything else is zero
features[desc.get_location(("X", "H"))] = 0
features[desc.get_location(("X", "O"))] = 0
self.assertEqual(features.sum(), 0)
def test_k2_peaks_periodic(self):
"""Tests the correct peak locations and intensities are found for the
k=2 term in periodic systems.
"""
atoms = Atoms(cell=[
[10, 0, 0],
[10, 10, 0],
[10, 0, 10],
],
symbols=["H", "C"],
scaled_positions=[
[0.1, 0.5, 0.5],
[0.9, 0.5, 0.5],
])
desc = LMBTR(species=["H", "C"],
k2={
"geometry": {
"function": "distance"
},
"grid": {
"min": 0,
"max": 10,
"sigma": 0.5,
"n": 1000
},
"weighting": {
"function": "exp",
"scale": 0.8,
"cutoff": 1e-3
},
},
normalize_gaussians=False,
periodic=True,
flatten=True,
sparse=False)
features = desc.create(atoms, [0])[0, :]
x = desc.get_k2_axis()
# Calculate assumed locations and intensities.
assumed_locs = np.array([2, 8])
assumed_ints = np.exp(-0.8 * np.array([2, 8]))
# Check the X-C peaks
xc_feat = features[desc.get_location(("X", "C"))]
xc_peak_indices = find_peaks(xc_feat, prominence=0.001)[0]
xc_peak_locs = x[xc_peak_indices]
xc_peak_ints = xc_feat[xc_peak_indices]
self.assertTrue(
np.allclose(xc_peak_locs, assumed_locs, rtol=0, atol=1e-2))
self.assertTrue(
np.allclose(xc_peak_ints, assumed_ints, rtol=0, atol=1e-2))
# Check that everything else is zero
features[desc.get_location(("X", "C"))] = 0
self.assertEqual(features.sum(), 0)
def test_k3_peaks_finite(self):
"""Tests the correct peak locations and intensities are found for the
k=3 term in finite systems.
"""
desc = LMBTR(
species=["H", "O"],
k3={
"geometry": {"function": "angle"},
"grid": {"min": -10, "max": 180, "sigma": 5, "n": 2000},
"weighting": {"function": "unity"},
},
normalize_gaussians=False,
periodic=False,
flatten=True,
sparse=False
)
features = desc.create(H2O, [0])[0, :]
x = desc.get_k3_axis()
# Check the X-H-O peaks
xho_assumed_locs = np.array([38])
xho_assumed_ints = np.array([1])
xho_feat = features[desc.get_location(("X", "H", "O"))]
xho_peak_indices = find_peaks(xho_feat, prominence=0.5)[0]
xho_peak_locs = x[xho_peak_indices]
xho_peak_ints = xho_feat[xho_peak_indices]
self.assertTrue(np.allclose(xho_peak_locs, xho_assumed_locs, rtol=0, atol=5e-2))
self.assertTrue(np.allclose(xho_peak_ints, xho_assumed_ints, rtol=0, atol=5e-2))
# Check the X-O-H peaks
xoh_assumed_locs = np.array([104])
xoh_assumed_ints = np.array([1])
xoh_feat = features[desc.get_location(("X", "O", "H"))]
xoh_peak_indices = find_peaks(xoh_feat, prominence=0.5)[0]
xoh_peak_locs = x[xoh_peak_indices]
xoh_peak_ints = xoh_feat[xoh_peak_indices]
self.assertTrue(np.allclose(xoh_peak_locs, xoh_assumed_locs, rtol=0, atol=5e-2))
self.assertTrue(np.allclose(xoh_peak_ints, xoh_assumed_ints, rtol=0, atol=5e-2))
# Check the H-X-O peaks
hxo_assumed_locs = np.array([38])
hxo_assumed_ints = np.array([1])
hxo_feat = features[desc.get_location(("H", "X", "O"))]
hxo_peak_indices = find_peaks(hxo_feat, prominence=0.5)[0]
hxo_peak_locs = x[hxo_peak_indices]
hxo_peak_ints = hxo_feat[hxo_peak_indices]
self.assertTrue(np.allclose(hxo_peak_locs, hxo_assumed_locs, rtol=0, atol=5e-2))
self.assertTrue(np.allclose(hxo_peak_ints, hxo_assumed_ints, rtol=0, atol=5e-2))
# Check that everything else is zero
features[desc.get_location(("X", "H", "O"))] = 0
features[desc.get_location(("X", "O", "H"))] = 0
features[desc.get_location(("H", "X", "O"))] = 0
self.assertEqual(features.sum(), 0)
def test_periodic(self):
"""LMBTR: Test periodic flag
"""
test_sys = Atoms(
cell=[[5.0, 0.0, 0.0], [0, 5.0, 0.0], [0.0, 0.0, 5.0]],
positions=[[0, 0, 1], [0, 0, 3]],
symbols=["H", "H"],
)
test_sys_ = Atoms(
cell=[[5.0, 0.0, 0.0], [0, 5.0, 0.0], [0.0, 0.0, 5.0]],
positions=[[0, 0, 1], [0, 0, 4]],
symbols=["H", "H"],
)
decay_factor = 0.5
lmbtr = LMBTR(species=[1],
k=[2],
periodic=True,
grid={
"k2": {
"min": 1 / 5,
"max": 1,
"sigma": 0.001,
"n": 200,
},
},
weighting={
"k2": {
"function": "exponential",
"scale": decay_factor,
"cutoff": 1e-3
},
},
virtual_positions=False,
flatten=False,
sparse=False)
desc = lmbtr.create(test_sys, positions=[0])
desc_ = lmbtr.create(test_sys_, positions=[0])
self.assertTrue(np.linalg.norm(desc_[0]["k2"] - desc[0]["k2"]) < 1e-6)
def test_flatten(self):
system = H2O
n = 10
n_elem = len(set(system.get_atomic_numbers())) + 1
# K2 unflattened
desc = LMBTR(species=[1, 8],
k=[2],
grid={"k2": {
"n": n,
"min": 0,
"max": 2,
"sigma": 0.1
}},
virtual_positions=False,
periodic=False,
flatten=False,
sparse=False)
# print(desc._atomic_numbers)
feat = desc.create(system, positions=[0])[0]["k2"]
self.assertEqual(feat.shape, (n_elem, n_elem, n))
# K2 flattened. The sparse matrix only supports 2D matrices, so the first
# dimension is always present, even if it is of length 1.
desc = LMBTR(species=[1, 8],
k=[2],
grid={"k2": {
"n": n,
"min": 0,
"max": 2,
"sigma": 0.1
}},
virtual_positions=False,
periodic=False,
flatten=True,
sparse=False)
feat = desc.create(system, positions=[0])
self.assertEqual(feat.shape,
(1, (1 / 2 * (n_elem) * (n_elem + 1) * n)))
def test_sparse(self):
"""Tests the sparse matrix creation.
"""
# Dense
desc = LMBTR(species=[1, 8],
k=[1],
grid=default_grid,
virtual_positions=False,
periodic=False,
flatten=True,
sparse=False)
vec = desc.create(H2O, positions=[0])
self.assertTrue(type(vec) == np.ndarray)
# Sparse
desc = LMBTR(species=[1, 8],
k=[1],
grid=default_grid,
virtual_positions=False,
periodic=False,
flatten=True,
sparse=True)
vec = desc.create(H2O, positions=[0])
self.assertTrue(type(vec) == scipy.sparse.coo_matrix)
def test_k3_peaks_periodic(self):
"""Tests the correct peak locations and intensities are found for the
k=3 term in periodic systems.
"""
scale = 0.85
desc = LMBTR(
species=["H"],
k3={
"geometry": {
"function": "angle"
},
"grid": {
"min": 0,
"max": 180,
"sigma": 5,
"n": 2000
},
"weighting": {
"function": "exp",
"scale": scale,
"cutoff": 1e-3
},
},
normalize_gaussians=False,
periodic=True,
flatten=True,
sparse=False,
)
atoms = Atoms(
cell=[
[10, 0, 0],
[0, 10, 0],
[0, 0, 10],
],
symbols=3 * ["H"],
scaled_positions=[
[0.05, 0.40, 0.5],
[0.05, 0.60, 0.5],
[0.95, 0.5, 0.5],
],
pbc=True,
)
features = desc.create(atoms, [0])[0, :]
x = desc.get_k3_axis()
# Calculate assumed locations and intensities.
assumed_locs = np.array([45, 90])
dist = 2 + 2 * np.sqrt(2) # The total distance around the three atoms
weight = np.exp(-scale * dist)
assumed_ints = np.array([weight, weight])
# Check the X-H-H peaks
xhh_feat = features[desc.get_location(("X", "H", "H"))]
xhh_peak_indices = find_peaks(xhh_feat, prominence=0.01)[0]
xhh_peak_locs = x[xhh_peak_indices]
xhh_peak_ints = xhh_feat[xhh_peak_indices]
self.assertTrue(
np.allclose(xhh_peak_locs, assumed_locs, rtol=0, atol=1e-1))
self.assertTrue(
np.allclose(xhh_peak_ints, assumed_ints, rtol=0, atol=1e-1))
# Calculate assumed locations and intensities.
assumed_locs = np.array([45])
dist = 2 + 2 * np.sqrt(2) # The total distance around the three atoms
weight = np.exp(-scale * dist)
assumed_ints = np.array([weight])
# Check the H-X-H peaks
hxh_feat = features[desc.get_location(("H", "X", "H"))]
hxh_peak_indices = find_peaks(hxh_feat, prominence=0.01)[0]
hxh_peak_locs = x[hxh_peak_indices]
hxh_peak_ints = hxh_feat[hxh_peak_indices]
self.assertTrue(
np.allclose(hxh_peak_locs, assumed_locs, rtol=0, atol=1e-1))
self.assertTrue(
np.allclose(hxh_peak_ints, assumed_ints, rtol=0, atol=1e-1))
# Check that everything else is zero
features[desc.get_location(("X", "H", "H"))] = 0
features[desc.get_location(("H", "X", "H"))] = 0
self.assertEqual(features.sum(), 0)
"function": "exponential",
"scale": 0.5,
"cutoff": 1e-3
},
},
periodic=False,
normalization="l2_each",
)
# Create
from ase.build import molecule
water = molecule("H2O")
# Create MBTR output for the system
mbtr_water = lmbtr.create(water, positions=[0])
print(mbtr_water)
print(mbtr_water.shape)
# Surface sites
# Build a surface and extract different adsorption positions
from ase.build import fcc111, add_adsorbate
slab_pure = fcc111('Al', size=(2, 2, 3), vacuum=10.0)
slab_ads = slab_pure.copy()
add_adsorbate(slab_ads, 'H', 1.5, 'ontop')
ontop_pos = slab_ads.get_positions()[-1]
add_adsorbate(slab_ads, 'H', 1.5, 'bridge')
bridge_pos = slab_ads.get_positions()[-1]
add_adsorbate(slab_ads, 'H', 1.5, 'hcp')
hcp_pos = slab_ads.get_positions()[-1]
def main(fxyz, dictxyz, prefix, output, per_atom, config_path, periodic, stride):
"""
Generate the LMBTR Representation.
Parameters
----------
fxyz: string giving location of xyz file
dictxyz: string giving location of xyz file that is used as a dictionary
prefix: string giving the filename prefix
output: [xyz]: append the representations to extended xyz file; [mat] output as a standlone matrix
param_path': string Specify the Kn parameters using a json file. (see https://singroup.github.io/dscribe/tutorials/lmbtr.html)
periodic: string (True or False) indicating whether the system is periodic
stride: compute descriptor each X frames
"""
periodic = bool(periodic)
per_atom = bool(per_atom)
fframes = []
dictframes = []
# read frames
if fxyz != 'none':
fframes = read(fxyz, slice(0, None, stride))
nfframes = len(fframes)
print("read xyz file:", fxyz, ", a total of", nfframes, "frames")
# read frames in the dictionary
if dictxyz != 'none':
dictframes = read(dictxyz, ':')
ndictframes = len(dictframes)
print("read xyz file used for a dictionary:", dictxyz, ", a total of",
ndictframes, "frames")
frames = dictframes + fframes
nframes = len(frames)
global_species = []
for frame in frames:
global_species.extend(frame.get_atomic_numbers())
if not periodic:
frame.set_pbc([False, False, False])
global_species = np.unique(global_species)
print("a total of", nframes, "frames, with elements: ", global_species)
if config_path:
try:
with open(config_path, 'r') as config_file:
config = json.load(config_file)
except Exception:
raise IOError('Cannot load the json file for parameters')
if config_path:
rep_atomic = LMBTR(species=global_species, periodic=periodic, flatten=True, **config)
else:
rep_atomic = LMBTR(species=global_species, flatten=True, periodic=periodic)
if config_path:
foutput = prefix + '-' + config_path
desc_name = "LMBTR" + '-' + config_path
else:
foutput = prefix
desc_name = "LMBTR"
# prepare for the output
if os.path.isfile(foutput + ".xyz"): os.rename(foutput + ".xyz", "bck." + foutput + ".xyz")
if os.path.isfile(foutput + ".desc"): os.rename(foutput + ".desc", "bck." + foutput + ".desc")
for i, frame in enumerate(frames):
fnow = rep_atomic.create(frame)
frame.info[desc_name] = fnow.mean(axis=0)
# save
if output == 'matrix':
with open(foutput + ".desc", "ab") as f:
np.savetxt(f, frame.info[desc_name][None])
if per_atom or nframes == 1:
with open(foutput + ".atomic-desc", "ab") as fatomic:
np.savetxt(fatomic, fnow)
elif output == 'xyz':
# output per-atom info
if per_atom:
frame.new_array(desc_name, fnow)
# write xyze
write(foutput + ".xyz", frame, append=True)
else:
raise ValueError('Cannot find the output format')
"scale": decay_factor,
"cutoff": 1e-3
},
"k3": {
"function": "exponential",
"scale": decay_factor,
"cutoff": 1e-3
},
},
sparse=False,
flatten=False
)
# The output of local MBTR is a list of atomic environments for each given
# position
desc = mbtr.create(NaCl_conv, positions=[3])
# Create variable contains the mapping between an index in the output and the
# corresponding atomic number
elements = NaCl_conv.get_atomic_numbers().tolist()
elements.append(0) # We add the ghost atom element
n_elements = len(set(elements))
imap = mbtr.index_to_atomic_number
smap = {}
for index, number in imap.items():
smap[index] = ase.data.chemical_symbols[number]
# Plot K2. Only the combinations i-j where j >= 1 are included in the output.
# The combination where i > i would contain the same information due to
# distance symmetry with respect to changing the indices.
x2 = mbtr._axis_k2
def test_parallel_sparse(self):
"""Tests creating sparse output parallelly.
"""
# Test indices
samples = [molecule("CO"), molecule("N2O")]
desc = LMBTR(species=[6, 7, 8],
k=[2],
grid={"k2": {
"n": 100,
"min": 0,
"max": 2,
"sigma": 0.1
}},
virtual_positions=False,
periodic=False,
flatten=True,
sparse=True)
n_features = desc.get_number_of_features()
# Multiple systems, serial job
output = desc.create(
system=samples,
positions=[[0], [0, 1]],
n_jobs=1,
).toarray()
assumed = np.empty((3, n_features))
assumed[0, :] = desc.create(samples[0], [0]).toarray()
assumed[1, :] = desc.create(samples[1], [0]).toarray()
assumed[2, :] = desc.create(samples[1], [1]).toarray()
self.assertTrue(np.allclose(output, assumed))
# Test when position given as indices
output = desc.create(
system=samples,
positions=[[0], [0, 1]],
n_jobs=2,
).toarray()
assumed = np.empty((3, n_features))
assumed[0, :] = desc.create(samples[0], [0]).toarray()
assumed[1, :] = desc.create(samples[1], [0]).toarray()
assumed[2, :] = desc.create(samples[1], [1]).toarray()
self.assertTrue(np.allclose(output, assumed))
# Test with cartesian positions. In this case virtual positions have to
# be enabled
desc = LMBTR(species=[6, 7, 8],
k=[2],
grid={"k2": {
"n": 100,
"min": 0,
"max": 2,
"sigma": 0.1
}},
virtual_positions=True,
periodic=False,
flatten=True,
sparse=True)
output = desc.create(
system=samples,
positions=[[[0, 0, 0], [1, 2, 0]], [[1, 2, 0]]],
n_jobs=2,
).toarray()
assumed = np.empty((2 + 1, n_features))
assumed[0, :] = desc.create(samples[0], [[0, 0, 0]]).toarray()
assumed[1, :] = desc.create(samples[0], [[1, 2, 0]]).toarray()
assumed[2, :] = desc.create(samples[1], [[1, 2, 0]]).toarray()
self.assertTrue(np.allclose(output, assumed))
def test_positions(self):
"""Tests that the position argument is handled correctly. The position
can be a list of integers or a list of 3D positions.
"""
decay_factor = 0.5
lmbtr = LMBTR(species=[1, 8],
k=[1, 2],
grid={
"k1": {
"min": 10,
"max": 18,
"sigma": 0.1,
"n": 200,
},
"k2": {
"min": 0,
"max": 0.7,
"sigma": 0.01,
"n": 200,
},
"k3": {
"min": -1.0,
"max": 1.0,
"sigma": 0.05,
"n": 200,
}
},
weighting={
"k2": {
"function": "exponential",
"scale": decay_factor,
"cutoff": 1e-3
},
"k3": {
"function": "exponential",
"scale": decay_factor,
"cutoff": 1e-3
},
},
periodic=True,
virtual_positions=True,
flatten=False,
sparse=False)
# Position as a cartesian coordinate in list
lmbtr.create(H2O, positions=[[0, 1, 0]])
# Position as a cartesian coordinate in numpy array
lmbtr.create(H2O, positions=np.array([[0, 1, 0]]))
# Position as a scaled coordinate in list
lmbtr.create(H2O, positions=[[0, 0, 0.5]], scaled_positions=True)
# Position as a scaled coordinate in numpy array
lmbtr.create(H2O,
positions=np.array([[0, 0, 0.5]]),
scaled_positions=True)
# Positions as lists of vectors
positions = [[0, 1, 2], [0, 0, 0]]
desc = lmbtr.create(H2O, positions)
# Position outside range
with self.assertRaises(ValueError):
lmbtr.create(H2O, positions=[3])
# Invalid data type
with self.assertRaises(ValueError):
lmbtr.create(H2O, positions=['a'])
# Cannot use scaled positions without cell information
with self.assertRaises(ValueError):
H = Atoms(
positions=[[0, 0, 0]],
symbols=["H"],
)
lmbtr.create(H, positions=[[0, 0, 1]], scaled_positions=True)
# Non-virtual positions
lmbtr = LMBTR(species=[1, 8],
k=[3],
grid=default_grid,
virtual_positions=False,
periodic=False,
flatten=True)
# Positions as a list of integers pointing to atom indices
positions = [0, 1, 2]
desc = lmbtr.create(H2O, positions)