def get_rdf_A_B(types, atoms, listTypeName, listTypeNum, rMax, nBins = 200):
#get index of element types of interest
typeIndex=[]
for iType in types:
for j in range(len(listTypeName)):
if iType == listTypeName[j]:
typeIndex.append(j)
typeAStart = 0
typeAEnd = 0
for i in range(len(listTypeNum)):
if i < typeIndex[0]:
typeAStart += listTypeNum[i]
typeAEnd = typeAStart + listTypeNum[typeIndex[0]]
#print(types[0],typeAStart,typeAEnd)
typeBStart = 0
typeBEnd = 0
for i in range(len(listTypeNum)):
if i < typeIndex[1]:
typeBStart += listTypeNum[i]
typeBEnd = typeBStart + listTypeNum[typeIndex[1]]
#print(types[1],typeBStart,typeBEnd)
atoms_A = atoms[typeAStart:typeAEnd]
atoms_B = atoms[typeBStart:typeBEnd]
atoms_new = atoms_A + atoms_B
d = neighborlist.neighbor_list('d', atoms_new, rMax)
dr = rMax/nBins
edges = np.arange(0., rMax + 1.1 *dr, dr)
h, binEdges = np.histogram(d, edges)
rho = len(atoms_new) / atoms.get_volume()
factor = 4./3. * np.pi * rho * len(atoms_new)
rdf = h / (factor * (binEdges[1:]**3 - binEdges[:-1]**3))
plt.plot(binEdges[1:], rdf)
plt.savefig('RDFADF/rdf_'+types[0]+'_'+types[1]+'.pdf')
plt.close()
peaks = (np.diff(np.sign(np.diff(rdf))) < 0).nonzero()[0] + 1 # local max
firstPeakInd = np.argmax(rdf[peaks])
firstPeak = binEdges[peaks[firstPeakInd]]
#peaks_2 = np.delete(peaks, firstPeakInd)
#secondPeakInd = np.argmax(rdf[peaks_2])
#secondPeak = binEdges[peaks_2[secondPeakInd]]
print("first peak of rdf: %12.8f" % firstPeak)
#print("second peak of rdf: %12.8f" % secondPeak)
#cutoff = (firstPeak + secondPeak)/2.0
cutoff = firstPeak*1.2
print("first NN cutoff set to: %12.8f" % cutoff)
#calculate CN
NBList = neighborlist.neighbor_list('ij', atoms_new, cutoff)
nnn = np.bincount(NBList[0]) #number of nearesr neighbors
typeA_CN = np.mean(nnn[:len(atoms_A)])
typeB_CN = np.mean(nnn[len(atoms_A):])
print("CN of %s : %8.6f" % (types[0], typeA_CN))
print("CN of %s : %8.6f" % (types[1], typeB_CN))
return(cutoff)
def water_O_idx(self):
# guess the o index of water
i = neighbor_list('i', self.poses[0], {('O', 'H'): 1.3})
j = neighbor_list('j', self.poses[0], {('O', 'H'): 1.3})
cn = np.bincount(i)
H2O_pair_list = []
Ow_idx = np.where(cn == 2)[0]
np.savetxt(os.path.join(os.path.dirname(self.xyz_file), "Ow_idx.dat"),
Ow_idx,
fmt='%d')
return Ow_idx
def test_single_site_crystal_large_cutoff(crystal, ase_env, torch_env):
cutoff = 2.0
ase_env.cutoff = cutoff
torch_env.cutoff = cutoff
idx_i, idx_j, idx_S, dist = neighbor_list("ijSd",
crystal,
ase_env.cutoff,
self_interaction=False)
nbh_ase, offsets_ase = ase_env.get_environment(crystal)
nbh_torch, offsets_torch = torch_env.get_environment(crystal)
# get number of neighbors from index vector
n_nbh = (np.unique(
np.hstack((idx_i, np.arange(crystal.get_global_number_of_atoms()))),
return_counts=True,
)[1] - 1)
# get number of neighbors from nbh matrix
n_nbh_ase_env = np.sum(nbh_ase >= 0, 1)
n_nbh_torch_env = np.sum(nbh_torch >= 0, 1)
# Compare the returned indices
nbh_ref = idx_j.reshape(crystal.get_global_number_of_atoms(), -1)
sorted_nbh_ref = np.sort(nbh_ref, axis=-1)
sorted_nbh_ase = np.sort(nbh_ase, axis=-1)
sorted_nbh_torch = np.sort(nbh_torch, axis=-1)
assert n_nbh.shape == n_nbh_ase_env.shape == n_nbh_torch_env.shape
assert np.allclose(n_nbh, n_nbh_ase_env)
assert np.allclose(n_nbh, n_nbh_torch_env)
assert np.allclose(sorted_nbh_ref, sorted_nbh_ase)
assert np.allclose(sorted_nbh_ref, sorted_nbh_torch)
assert np.allclose(sorted_nbh_ase, sorted_nbh_torch)
def test_clist_nl():
"""Cell list neighbor test
Compare with ASE implementation
"""
from ase.build import bulk
from ase.neighborlist import neighbor_list
from pinn.layers import cell_list_nl
to_test = [bulk('Cu'), bulk('Mg'), bulk('Fe')]
ind, coord, cell = [], [], []
for i, a in enumerate(to_test):
ind.append([[i]] * len(a))
coord.append(a.positions)
cell.append(a.cell)
with tf.Graph().as_default():
tensors = {
'ind_1': tf.constant(np.concatenate(ind, axis=0), tf.int32),
'coord': tf.constant(np.concatenate(coord, axis=0), tf.float32),
'cell': tf.constant(np.stack(cell, axis=0), tf.float32)
}
nl = cell_list_nl(tensors, rc=10)
with tf.Session() as sess:
dist_pinn = sess.run(nl['dist'])
dist_ase = []
for a in to_test:
dist_ase.append(neighbor_list('d', a, 10))
dist_ase = np.concatenate(dist_ase, 0)
assert np.all(np.sort(dist_ase) - np.sort(dist_pinn) < 1e-4)
def get_environment(self, atoms, grid=None):
if grid is not None:
raise NotImplementedError
n_atoms = atoms.get_global_number_of_atoms()
idx_i, idx_j, idx_S = neighbor_list(
"ijS", atoms, self.cutoff, self_interaction=False
)
if idx_i.shape[0] > 0:
uidx, n_nbh = np.unique(idx_i, return_counts=True)
n_max_nbh = np.max(n_nbh)
n_nbh = np.tile(n_nbh[:, np.newaxis], (1, n_max_nbh))
nbh_range = np.tile(
np.arange(n_max_nbh, dtype=np.int)[np.newaxis], (n_nbh.shape[0], 1)
)
mask = np.zeros((n_atoms, np.max(n_max_nbh)), dtype=np.bool)
mask[uidx, :] = nbh_range < n_nbh
neighborhood_idx = -np.ones((n_atoms, np.max(n_max_nbh)), dtype=np.float32)
neighborhood_idx[mask] = idx_j
offset = np.zeros((n_atoms, np.max(n_max_nbh), 3), dtype=np.float32)
offset[mask] = idx_S
else:
neighborhood_idx = -np.ones((n_atoms, 1), dtype=np.float32)
offset = np.zeros((n_atoms, 1, 3), dtype=np.float32)
return neighborhood_idx, offset
def _get_all_bonds(self):
bonds_all = {}
group1 = []
group2 = []
for potential in self.bond_potentials:
for bond, params in self.potentials[potential].items():
if bond in bonds_all:
raise Exception("Error: Bond names have to be unique!")
group1 = [
a.index for a in self.atoms
if a.symbol in params["creation"]["group1"]
]
group2 = [
a.index for a in self.atoms
if a.symbol in params["creation"]["group2"]
]
neighbors = neighbor_list("ijd", self.atoms,
params["creation"]["distance"][1])
distances = params["creation"]["distance"]
bonds = self._generate_bonds(group1, group2, neighbors,
distances[0], distances[1])
bonds_all[bond] = bonds
print bonds_all.keys(), len(bonds_all.values()[0]), len(
bonds_all.values()[1])
return bonds_all
def get_lists(atoms):
# build neighbor list
nl = []
for i in range(len(atoms)):
nl.append([])
tokens_i, tokens_j = neighbor_list('ij', atoms, cutoff_table)
for i in range(len(tokens_i)):
nl[tokens_i[i]].append(tokens_j[i])
o = open('bonds.dat', 'w')
# build bond list
bond_list = []
for i in range(len(nl)):
if len(nl[i]) > 0:
ai = i
for j in range(len(nl[i])):
aj = nl[i][j]
if ai < aj:
bond_length = atoms.get_distance(ai, aj, mic=True)
bond_length = bond_length / 10.0
bond_list.append([ai, aj, bond_length])
o.write('%d %d %.4f\n' % (ai, aj, bond_length))
o.close()
n_bond = len(bond_list)
print(n_bond, "bond terms")
o = open('angles.dat', 'w')
angle_list = []
# build angle list
for i in range(len(nl)):
if len(nl[i]) > 1:
aj = i
for j in range(len(nl[i])):
ai = nl[i][j]
for k in nl[i][j + 1:]:
ak = k
angle = atoms.get_angle(ai, aj, ak, mic=True)
angle_list.append([ai, aj, ak, angle])
o.write('%d %d %d %.4f\n' % (ai, aj, ak, angle))
o.close()
n_angle = len(angle_list)
print(n_angle, "angle terms")
dihedral_list = []
# build dihedral ist
for i in bond_list:
dj, dk = i[0], i[1]
for j in nl[dj]:
if j != dk:
di = j
for k in nl[dk]:
if k != dj:
dl = k
angle = atoms.get_dihedral(di, dj, dk, dl, mic=True)
dihedral_list.append([di, dj, dk, dl, angle])
n_dihedral = len(dihedral_list)
print(n_dihedral, "diheral terms")
return nl, bond_list, angle_list, dihedral_list
def update_nbr_list(self):
"""Update neighbor list and the periodic reindexing
for the given Atoms object.
Args:
cutoff (float): maximum cutoff for which atoms are
considered interacting.
Returns:
nbr_list (torch.LongTensor)
offsets (torch.Tensor)
nxyz (torch.Tensor)
"""
if self.nbr_torch:
edge_from, edge_to, offsets = torch_nbr_list(self, self.cutoff, device=self.device, directed=self.directed)
nbr_list = torch.LongTensor(np.stack([edge_from, edge_to], axis=1))
else:
self.wrap()
edge_from, edge_to, offsets = neighbor_list('ijS', self, self.cutoff)
nbr_list = torch.LongTensor(np.stack([edge_from, edge_to], axis=1))
offsets = torch.Tensor(offsets)[nbr_list[:, 1] > nbr_list[:, 0]].detach().cpu().numpy()
nbr_list = nbr_list[nbr_list[:, 1] > nbr_list[:, 0]]
# torch.sparse has no storage yet.
#offsets = offsets.dot(self.get_cell())
offsets = sparsify_array(offsets.dot(self.get_cell()))
self.nbr_list = nbr_list
self.offsets = offsets
return nbr_list, offsets
def calculate(self, atoms=None, properties=['energy'],
system_changes=['positions', 'numbers', 'cell',
'pbc', 'charges', 'magmoms']):
Calculator.calculate(self, atoms, properties, system_changes)
epsilon = self.parameters.epsilon
rho0 = self.parameters.rho0
r0 = self.parameters.r0
rcut1 = self.parameters.rcut1 * r0
rcut2 = self.parameters.rcut2 * r0
forces = np.zeros((len(self.atoms), 3))
preF = - 2 * epsilon * rho0 / r0
i, j, d, D = neighbor_list('ijdD', atoms, rcut2)
dhat = (D / d[:, None]).T
expf = np.exp(rho0 * (1.0 - d / r0))
fc = fcut(d, rcut1, rcut2)
E = epsilon * expf * (expf - 2)
dE = preF * expf * (expf - 1) * dhat
energy = 0.5 * (E * fc).sum()
F = (dE * fc + E * fcut_d(d, rcut1, rcut2) * dhat).T
for dim in range(3):
forces[:, dim] = np.bincount(i, weights=F[:, dim],
minlength=len(atoms))
self.results['energy'] = energy
self.results['forces'] = forces
def cluster_size(fname):
traj = TrajectoryReader(fname)
sizes = []
num_neigh = 6
for atoms in traj:
first, second = neighbor_list('ij', atoms, cutoff=3.0)
cluster_size = 0
n_count = [0 for _ in range(len(first))]
for f, s in zip(first, second):
if atoms[f].symbol == 'Mg' and atoms[s].symbol == 'Si':
n_count[f] += 1
elif atoms[f].symbol == 'Si' and atoms[s].symbol == 'Mg':
n_count[f] += 1
cluster_size = sum(1 for n in n_count if n >= num_neigh)
sizes.append(cluster_size)
fig = plt.figure(figsize=(4, 3))
ax = fig.add_subplot(1, 1, 1)
ax.plot(sizes)
ax.set_xlabel("Time")
ax.set_ylabel("Fraction of solutes in cluster")
ax.spines['right'].set_visible(False)
ax.spines['top'].set_visible(False)
fig.tight_layout()
fig.savefig("data/kmc_growth.png", dpi=200)
plt.show()
def mgsi(initial=None, comment=None):
if initial is None:
pureAl = bulk('Al', cubic=True) * (N, N, N)
pureAl = wrap_and_sort_by_position(pureAl)
tags, _ = get_layers(pureAl, (0, 0, 1))
success = False
while not success:
print("Generating new initial precipitate")
initial, success = create_precipitate(pureAl.copy(), tags,
normal_radius)
db = dataset.connect(DB_NAME)
ref_tbl = db[REF]
vac_tbl = db[VAC]
sol_tbl = db[SOL]
comment_tbl = db[COMMENT]
runID = hex(random.randint(0, 2**32 - 1))
if comment is not None:
comment_tbl.insert({'runID': runID, 'comment': comment})
eci = {}
with open("data/almgsix_normal_ce.json", 'r') as infile:
data = json.load(infile)
eci = data['eci']
settings = settingsFromJSON("data/settings_almgsiX_voldev.json")
settings.basis_func_type = "binary_linear"
atoms = attach_calculator(settings, initial.copy(), eci)
atoms.numbers = initial.numbers
ref_energy = atoms.get_potential_energy()
ref_tbl.insert({'runID': runID, 'energy': ref_energy})
for atom in atoms:
if atom.symbol in ['Mg', 'Si']:
pos = atom.position
sol_tbl.insert({
'runID': runID,
'symbol': atom.symbol,
'X': pos[0],
'Y': pos[1],
'Z': pos[2]
})
ref, neighbors = neighbor_list('ij', atoms, 3.0)
for ref, nb in zip(ref, neighbors):
if atoms[ref].symbol == 'Al' and atoms[nb].symbol in ['Mg', 'Si']:
atoms[ref].symbol = 'X'
e = atoms.get_potential_energy()
atoms[ref].symbol = 'Al'
pos = atoms[ref].position
vac_tbl.insert({
'runID': runID,
'X': pos[0],
'Y': pos[1],
'Z': pos[2],
'energy': e
})
atoms = removeAl(atoms)
def save_nb_list(file_in,cutoff):
atoms = read(file_in)
nblist=neighborlist.neighbor_list('ijD', atoms, cutoff)
nnn = np.bincount(nblist[0]) #number of nearesr neighbors
import matplotlib.pyplot as plt
plt.hist(nnn, bins='auto')
plt.savefig('cn_dist.eps')
return(nnn,nblist[0],nblist[1],nblist[2])
def compute_sorted_distances_with_pbc(feature_parameters, frames,
center_atom_id_mask):
print("Warning: Sorted distances only works for one species")
cutoff = feature_parameters["interaction_cutoff"]
max_neighbors = 0
for frame_id in range(len(frames)):
frame = frames[frame_id]
atom_i = neighborlist.neighbor_list('i', frame, cutoff)
for atom_id in center_atom_id_mask[frame_id]:
max_neighbors = max(max_neighbors,
np.max(np.sum(atom_i == atom_id)))
padding_type = feature_parameters["padding_type"]
if padding_type == "max":
max_distance = cutoff
#for frame_id in range(len(frames)):
# frame = frames[frame_id]
# atom_i, distances = neighborlist.neighbor_list('id', frame, cutoff)
# for atom_id in center_atom_id_mask[frame_id]:
# max_distance = max(max_distance, np.max(distances[atom_i == atom_id]))
padding = max_distance
elif padding_type == "zero":
padding = 0
else:
raise ("Error padding_type " + padding_type + " is not available.")
sorted_distances = np.ones(
(sum([len(env_idx)
for env_idx in center_atom_id_mask]), max_neighbors)) * padding
k = 0
for frame_id in range(len(frames)):
frame = frames[frame_id]
atom_i, distances = neighborlist.neighbor_list('id', frame, cutoff)
for atom_id in center_atom_id_mask[frame_id]:
# solution to extract distances from structure to env assumes atom_i is sorted
sorted_distances_env = np.sort(distances[atom_i == atom_id])
sorted_distances[
k, :len(sorted_distances_env)] = sorted_distances_env
k += 1
return sorted_distances
def compute_rdf_cross(atom, cutoff_=5.0, nbins_=501, sym1_ = "O", sym2_ = "Si"):
"""
returns auto and cross-RDF for different spcies and bin_edges
"""
syms = np.asarray(atom.get_chemical_symbols())
idx_o = np.where(syms == sym1_)[0]
idx_s = np.where(syms == sym2_)[0]
bins = np.linspace(0.0, cutoff_ + 2, 501)
i, j, d, D = neighbor_list('ijdD', atom, cutoff=cutoff_, self_interaction=False)
rdf_list = []
_auxset = set(idx_o)
d_list = []
for idx in _auxset:
a = list(j[np.where(i == idx)[0]])
b = list(d[np.where(i == idx)[0]])
d_list = d_list + [b[a.index(x)] for x in a if x in _auxset]
h, bin_edges = np.histogram(d_list, bins)
rdf = h / len(idx_o)
rdf_list.append(rdf)
_auxset = set(idx_s)
d_list = []
for idx in _auxset:
a = list(j[np.where(i == idx)[0]])
b = list(d[np.where(i == idx)[0]])
d_list = d_list + [b[a.index(x)] for x in a if x in _auxset]
h, bin_edges = np.histogram(d_list, bins)
rdf = h / len(idx_s)
rdf_list.append(rdf)
_auxset = set(idx_s)
d_list = []
for idx in idx_o:
a = list(j[np.where(i == idx)[0]])
b = list(d[np.where(i == idx)[0]])
d_list = d_list + [b[a.index(x)] for x in a if x in _auxset]
h, bin_edges = np.histogram(d_list, bins)
rdf = h / len(idx_o)
rdf_list.append(rdf)
return rdf_list, bin_edges
def get_lists(atoms):
# build neighbor list
nl = []
for i in range(len(atoms)):
nl.append([])
tokens_i, tokens_j = neighbor_list('ij', atoms, cutoff_table)
for i in range(len(tokens_i)):
nl[tokens_i[i]].append(tokens_j[i])
# build bond list
bond_list = []
for i in range(len(nl)):
if len(nl[i]) > 0:
ai = i
for j in range(len(nl[i])):
aj = nl[i][j]
if ai < aj:
bond_list.append([ai, aj])
n_bond = len(bond_list)
print(n_bond, "bond terms")
angle_list = []
# build angle list
for i in range(len(nl)):
if len(nl[i]) > 1:
aj = i
for j in range(len(nl[i])):
ai = nl[i][j]
for k in nl[i][j + 1:]:
ak = k
angle_list.append([ai, aj, ak])
n_angle = len(angle_list)
print(n_angle, "angle terms")
dihedral_list = []
# build dihedral ist
for i in bond_list:
dj, dk = i[0], i[1]
for j in nl[dj]:
if j != dk:
di = j
for k in nl[dk]:
if k != dj:
dl = k
dihedral_list.append([di, dj, dk, dl])
n_dihedral = len(dihedral_list)
print(n_dihedral, "diheral terms")
return nl, bond_list, angle_list, dihedral_list
def update_atoms_nbr_list(self, cutoff):
Atoms_list = self.get_list_atoms()
intra_nbr_list = []
for i, atoms in enumerate(Atoms_list):
edge_from, edge_to = neighbor_list('ij', atoms, cutoff)
nbr_list = torch.LongTensor(np.stack([edge_from, edge_to], axis=1))
nbr_list = nbr_list[nbr_list[:, 1] > nbr_list[:, 0]]
intra_nbr_list.append(
self.props['num_subgraphs'][: i].sum() + nbr_list)
intra_nbr_list = torch.cat(intra_nbr_list)
self.atoms_nbr_list = intra_nbr_list
def covariance_matrix(A, B):
neighbors_A = neighbor_list('ijDd', A, opt.rc)
neighbors_B = neighbor_list('ijDd', B, opt.rc)
i_list = set(neighbors_A[0])
if opt.nocenter is not None:
i_list = [i for i in i_list if A[i].number not in opt.nocenter]
j_list = set(neighbors_B[0])
if opt.nocenter is not None:
j_list = [j for j in j_list if B[j].number not in opt.nocenter]
size = (len(i_list), len(j_list))
covariance_matrix = np.zeros(size)
for ei, i in enumerate(i_list):
environment_i = environment(neighbors_A, i)
for ej, j in enumerate(j_list):
environment_j = environment(neighbors_B, j)
covariance_matrix[ei,
ej] = environment_kernel(environment_i,
environment_j)
return covariance_matrix
def compute_rdf(atom, cutoff =5.0, nbins =1001):
"""
returns RDF and bin_edges
"""
N = len(atom)
bins = np.linspace(0.0, cutoff + 2, nbins)
i, j, d, D = neighbor_list('ijdD', atom, cutoff=cutoff, self_interaction=False)
h, bin_edges = np.histogram(d, bins)
rdf = h / N
return rdf, bin_edges
def check_atoms_too_close(atoms):
# (Empty atoms with neighbor_list is buggy in ASE-3.16.0)
if not len(atoms):
return
# Skip test for numpy < 1.13.0 due to absence np.divmod:
if not hasattr(np, 'divmod'):
return
from ase.neighborlist import neighbor_list
from ase.data import covalent_radii
radii = covalent_radii[atoms.numbers] * 0.01
dists = neighbor_list('d', atoms, radii)
if len(dists):
raise AtomsTooClose('Atoms are too close, e.g. {} Å'.format(dists[0]))
def test_single_site_crystal_large_cutoff(crystal, ase_env):
ase_env.cutoff = 0.7
idx_i, idx_j, idx_S, dist = neighbor_list('ijSd', crystal, ase_env.cutoff,
self_interaction=False)
nbh_ase, offsets_ase = ase_env.get_environment(0, crystal)
# get number of neighbors from index vector
n_nbh = np.unique(np.hstack((idx_i, np.arange(crystal.get_number_of_atoms()))), return_counts=True)[1]-1
# get number of neighbors from nbh matrix
n_nbh_env = np.sum(nbh_ase >= 0, 1)
assert n_nbh.shape == n_nbh_env.shape
assert np.allclose(n_nbh, n_nbh_env)
def nl_cutoff_cov_vdw(sim_box, cut_off, vdw_cut_off=1.0, cov_cut_off=1.0):
overlap_vdwr_sphere = np.array([vdw_radii[atomic_numbers[x]]
for x in sim_box.get_chemical_symbols()])
overlap_covr_sphere = np.array([covalent_radii[atomic_numbers[x]]
for x in sim_box.get_chemical_symbols()])
overlap_sphere = cut_off * \
(vdw_cut_off * overlap_vdwr_sphere +
cov_cut_off * overlap_covr_sphere)/2
# for atoms without vdwr
overlap_sphere[np.isnan(overlap_vdwr_sphere)
] = cut_off * cov_cut_off * overlap_covr_sphere[np.isnan(overlap_vdwr_sphere)]
i, j = neighbor_list('ij', sim_box, overlap_sphere, self_interaction=False)
return i, j
def get_nij_and_nijk(atoms, rc, angular=False):
ilist, jlist = neighbor_list('ij', atoms, cutoff=rc)
nij = len(ilist)
if angular:
nl = {}
for i, atomi in enumerate(ilist):
if atomi not in nl:
nl[atomi] = []
nl[atomi].append(jlist[i])
nijk = 0
for atomi, nlist in nl.items():
n = len(nlist)
nijk += (n - 1 + 1) * (n - 1) // 2
else:
nijk = 0
return nij, nijk
def update_system_nbr_list(self, cutoff, exclude_atoms_nbr_list=True):
"""Update undirected neighbor list and the periodic reindexing
for the given Atoms object.ß
Args:
cutoff (float): maximum cutoff for which atoms are
considered interacting.
Returns:
nbr_list (torch.LongTensor)
offsets (torch.Tensor)
nxyz (torch.Tensor)
"""
if self.nbr_torch:
edge_from, edge_to, offsets = torch_nbr_list(self,
cutoff,
device=self.device)
nbr_list = torch.LongTensor(np.stack([edge_from, edge_to], axis=1))
else:
edge_from, edge_to, offsets = neighbor_list('ijS', self, cutoff)
nbr_list = torch.LongTensor(np.stack([edge_from, edge_to], axis=1))
offsets = torch.Tensor(offsets)[nbr_list[:, 1] > nbr_list[:, 0]]
nbr_list = nbr_list[nbr_list[:, 1] > nbr_list[:, 0]]
if exclude_atoms_nbr_list:
offsets_mat = torch.zeros(self.get_number_of_atoms(),
self.get_number_of_atoms(), 3)
nbr_list_mat = torch.zeros(self.get_number_of_atoms(),
self.get_number_of_atoms()).to(
torch.long)
atom_nbr_list_mat = torch.zeros(self.get_number_of_atoms(),
self.get_number_of_atoms()).to(
torch.long)
offsets_mat[nbr_list[:, 0], nbr_list[:, 1]] = offsets
nbr_list_mat[nbr_list[:, 0], nbr_list[:, 1]] = 1
atom_nbr_list_mat[self.atoms_nbr_list[:, 0],
self.atoms_nbr_list[:, 1]] = 1
nbr_list_mat = nbr_list_mat - atom_nbr_list_mat
nbr_list = nbr_list_mat.nonzero()
offsets = offsets_mat[nbr_list[:, 0], nbr_list[:, 1], :]
self.nbr_list = nbr_list
self.offsets = sparsify_array(
offsets.matmul(torch.Tensor(self.get_cell())))
def compute_rdf_subset(atoms, indexes, cutoff=6.0, nbins=201):
"""
returns RDF computer over a subset of atoms and bin_edges
"""
i, j, d, D = neighbor_list('ijdD', atoms, cutoff=6, self_interaction=False)
dlist = []
for idx in indexes:
dlist.append(d[np.where(i == idx)[0]])
dlist = np.concatenate(dlist, axis=0)
bins = np.linspace(0.0, cutoff+2, nbins)
N = len(indexes)
h, bin_edges = np.histogram(dlist, bins)
rdf = h / N
return rdf, bin_edges
def __init__(self, atoms, cutoff=4.0, elements=[]):
from ase.neighborlist import neighbor_list
self.atoms = atoms
self.cutoff = cutoff
self.elements = elements
first_indx, second_indx, self.dist = neighbor_list(
"ijd", atoms, cutoff)
# neighbors
self.neighbors = [[] for _ in range(len(self.atoms))]
for i1, i2 in zip(first_indx, second_indx):
self.neighbors[i1].append(i2)
# Count how many pairs inside cutoff
self.num_pairs = self.num_pairs_brute_force()
self.avg_num_pairs = 0
self.num_calls = 0
self.symbols = [atom.symbol for atom in self.atoms]
def fingerprint(images, cutoff, etas, Rc, elements, cutoff_function=False):
for count, atoms in enumerate(images):
species = sorted(list(set(atoms.get_chemical_symbols())))
N_atoms = len(atoms)
N_species = len(species)
N_etas = len(etas)
neighbors = neighbor_list('ijdD', atoms, cutoff / 2 * np.ones(N_atoms))
for i, atom in enumerate(atoms):
if atom.symbol in elements:
fingerprint = np.zeros([3, N_species, N_etas])
for j, element in enumerate(species):
for k, (eta, R) in enumerate(zip(etas, Rc)):
indices = np.argwhere(neighbors[0] == atom.index)
neighbor_indices = neighbors[1][
indices] #get indices of neighbor atoms
for index, neighbor_index in zip(
indices, neighbor_indices):
if atoms[neighbor_index[0]].symbol == element:
Rij = neighbors[2][index[
0]] #distance from central atom to neighbor
rij = neighbors[3][index[
0]] #distances vector from central atom to neighbor
if cutoff_function:
fingerprint[:, j, k] += rij / Rij * np.exp(
-((Rij - R) / eta)**2) * 0.5 * (
np.cos(np.pi * Rij / cutoff) + 1)
else:
fingerprint[:, j,
k] += rij / Rij * np.exp(-(
(Rij - R) / eta)**2)
fingerprint = fingerprint.reshape(3, N_species * N_etas)
try:
fingerprints = np.concatenate((fingerprints, fingerprint),
axis=0)
except UnboundLocalError: #fingerprints not defined in very first iteration
fingerprints = fingerprint
else:
continue
return fingerprints
def get_neighbours(atoms,
r_cut,
self_interaction=False,
neighbor_list=neighbor_list):
"""Return a list of pairs of atoms within a given distance of each other.
Uses ase.neighborlist.neighbour_list to compute neighbors.
Args:
atoms: ase.atoms object to calculate neighbours for
r_cut: cutoff radius (float). Pairs of atoms are considered neighbours
if they are within a distance r_cut of each other (note that this
is double the parameter used in the ASE's neighborlist module)
neighbor_list: function (optional). Optionally replace the built-in
ASE neighbour list with an alternative with the same call
signature, e.g. `matscipy.neighbours.neighbour_list`.
Returns: a tuple (i_list, j_list, d_list, fixed_atoms):
i_list, j_list: i and j indices of each neighbour pair
d_list: absolute distance between the corresponding pair
fixed_atoms: indices of any fixed atoms
"""
if isinstance(atoms, Filter):
atoms = atoms.atoms
i_list, j_list, d_list = neighbor_list('ijd', atoms, r_cut)
# filter out self-interactions (across PBC)
if not self_interaction:
mask = i_list != j_list
i_list = i_list[mask]
j_list = j_list[mask]
d_list = d_list[mask]
# filter out bonds where 1st atom (i) in pair is fixed
fixed_atoms = []
for constraint in atoms.constraints:
if isinstance(constraint, FixAtoms):
fixed_atoms.extend(list(constraint.index))
return i_list, j_list, d_list, fixed_atoms
def get_g2_map(atoms: Atoms,
rc: float,
nij_max: int,
interactions: list,
vap: VirtualAtomMap,
offsets: np.ndarray,
for_prediction=False,
print_time=False):
if for_prediction:
iaxis = 0
else:
iaxis = 1
g2_map = np.zeros((nij_max, iaxis + 2), dtype=np.int32)
tlist = np.zeros(nij_max, dtype=np.int32)
symbols = atoms.get_chemical_symbols()
tic = time.time()
ilist, jlist, n1 = neighbor_list('ijS', atoms, rc)
if print_time:
print(f"* ASE neighbor time: {time.time() - tic}")
nij = len(ilist)
tlist.fill(0)
for i in range(nij):
symboli = symbols[ilist[i]]
symbolj = symbols[jlist[i]]
tlist[i] = interactions.index('{}{}'.format(symboli, symbolj))
ilist = np.pad(ilist + 1, (0, nij_max - nij), 'constant')
jlist = np.pad(jlist + 1, (0, nij_max - nij), 'constant')
n1 = np.pad(n1, ((0, nij_max - nij), (0, 0)), 'constant')
n1 = n1.astype(np.float32)
for count in range(len(ilist)):
if ilist[count] == 0:
break
ilist[count] = vap.index_map[ilist[count]]
jlist[count] = vap.index_map[jlist[count]]
g2_map[:, iaxis + 0] = ilist
g2_map[:, iaxis + 1] = offsets[tlist]
return {
"g2.v2g_map": g2_map,
"g2.ilist": ilist,
"g2.jlist": jlist,
"g2.shift": n1
}
def compute_neighbors(self, cutoff):
if self._last_cutoff == cutoff:
return
self._pairs = []
nl_result = neighborlist.neighbor_list("ijdD", self._atoms, cutoff)
for (i, j, d, D) in zip(*nl_result):
if j < i:
# we want a half neighbor list, so drop all duplicated
# neighbors
continue
self._pairs.append((i, j, d, D))
self._pairs_by_center = []
for _ in range(self.size()):
self._pairs_by_center.append([])
for (i, j, d, D) in self._pairs:
self._pairs_by_center[i].append((i, j, d, D))
self._pairs_by_center[j].append((i, j, d, D))
def get_BOList(listTypeName, listTypeNum, atoms, cutoff):
NBList = neighborlist.neighbor_list('ijDd', atoms, cutoff)
nnn = np.bincount(NBList[0]) #number of nearesr neighbors
MType = 'Si'
typeIndex=[]
for j in range(len(listTypeName)):
if MType == listTypeName[j]:
typeIndex.append(j)
MTypeStart = 0
MTypeEnd = 0
for i in range(len(listTypeNum)):
if i < typeIndex[0]:
MTypeStart += listTypeNum[i]
MTypeEnd = MTypeStart + listTypeNum[typeIndex[0]]
OType = 'O'
typeIndex=[]
for j in range(len(listTypeName)):
if 'O' == listTypeName[j]:
typeIndex.append(j)
OTypeStart = 0
OTypeEnd = 0
for i in range(len(listTypeNum)):
if i < typeIndex[0]:
OTypeStart += listTypeNum[i]
OTypeEnd = OTypeStart + listTypeNum[typeIndex[0]]
OList = np.arange(OTypeStart, OTypeEnd)
OIndexList = ((NBList[1] >= OTypeStart) &\
(NBList[1] < OTypeEnd)).nonzero()[0]
BOList = []
for i in OList:
if nnn[i] >=2:
currentIndex = (NBList[0] == i).nonzero()[0]
count = 0
for j in (currentIndex):
if (NBList[1][j] >= MTypeStart) and (NBList[1][j] < MTypeEnd):
count += 1;
if count == 2:
BOList.append(i)
NBOList = list(set(OList) - set(BOList))
return(BOList, NBOList)