def test_atoms_distance():
# Setup a chain of H,O,C
# H-O Dist = 2
# O-C Dist = 3
# C-H Dist = 5 with mic=False
# C-H Dist = 4 with mic=True
a = Atoms('HOC', positions=[(1, 1, 1), (3, 1, 1), (6, 1, 1)])
a.set_cell((9, 2, 2))
a.set_pbc((True, False, False))
# Calculate indiviually with mic=True
assert a.get_distance(0, 1, mic=True) == 2
assert a.get_distance(1, 2, mic=True) == 3
assert a.get_distance(0, 2, mic=True) == 4
# Calculate indiviually with mic=False
assert a.get_distance(0, 1, mic=False) == 2
assert a.get_distance(1, 2, mic=False) == 3
assert a.get_distance(0, 2, mic=False) == 5
# Calculate in groups with mic=True
assert (a.get_distances(0, [1, 2], mic=True) == [2, 4]).all()
# Calculate in groups with mic=False
assert (a.get_distances(0, [1, 2], mic=False) == [2, 5]).all()
# Calculate all with mic=True
assert (a.get_all_distances(mic=True) == [[0, 2, 4],
[2, 0, 3],
[4, 3, 0]]).all()
# Calculate all with mic=False
assert (a.get_all_distances(mic=False) == [[0, 2, 5],
[2, 0, 3],
[5, 3, 0]]).all()
# Scale Distance
old = a.get_distance(0, 1)
a.set_distance(0, 1, 0.9, add=True, factor=True)
new = a.get_distance(0, 1)
diff = new - 0.9 * old
assert abs(diff) < 10e-6
# Change Distance
old = a.get_distance(0, 1)
a.set_distance(0, 1, 0.9, add=True)
new = a.get_distance(0, 1)
diff = new - old - 0.9
assert abs(diff) < 10e-6
def _calculate_distances(atoms: ase.Atoms,
min_im_conv: bool = True,
no_console: bool = False) -> np.array:
'''Calculates the distances between each pair of ions
By defaul it uses the minimum image convention
It returns a square array 'dist_array' with the distances
between ions i and j in dist_array[i][j]
'''
# calculate distances between the points in A
# D = atoms.get_all_distances(mic=True, simple=True) # eats up ALL the ram N=30 MAX
# TODO: parallelize
num_atoms = len(atoms)
dist_array = np.zeros((num_atoms, num_atoms), dtype=np.float64)
for i in tqdm(range(num_atoms),
unit='atoms',
total=num_atoms,
desc='Calculating distances',
disable=no_console):
dist_array[i, i:num_atoms] = atoms.get_distances(i,
range(i, num_atoms),
mic=min_im_conv)
# get the distance along the c axis divided by two
# dmaxReal = atoms.cell[2][2]/2;
# dist_array[dist_array > dmaxReal] = 0 # discard distances longer than dmax
dist_array = dist_array + dist_array.T # make symmetrical
# Ds_mic = get_all_distances(atoms)
# Ds = csr_matrix(dist_array)
return dist_array
def take_cluster(old_conf_name, type_map, idx, jdata):
cutoff = jdata['cluster_cutoff']
sys = dpdata.System(old_conf_name, fmt = 'lammps/dump', type_map = type_map)
atom_names = sys['atom_names']
atom_types = sys['atom_types']
cell = sys['cells'][0]
coords = sys['coords'][0]
symbols = [atom_names[atom_type] for atom_type in atom_types]
# detect fragment
frag_numb, frag_index, graph = _crd2frag(symbols, coords, True, cell, return_bonds=True)
# get_distances
all_atoms = Atoms(symbols = symbols, positions = coords, pbc=True, cell=cell)
all_atoms[idx].tag = 1
distances = all_atoms.get_distances(idx, range(len(all_atoms)), mic=True)
distancescutoff = distances < cutoff
cutoff_atoms_idx = np.where(distancescutoff)[0]
# make cutoff atoms in molecules
taken_atoms_idx = []
added = []
for ii in range(frag_numb):
frag_atoms_idx = np.where(frag_index == ii)[0]
if np.any(np.isin(frag_atoms_idx, cutoff_atoms_idx)):
if 'cluster_minify' in jdata and jdata['cluster_minify']:
# currently support C, H
take_frag_idx=[]
for aa in frag_atoms_idx:
if np.any(np.isin(aa, cutoff_atoms_idx)):
take_frag_idx.append(aa)
elif np.count_nonzero(np.logical_and(distancescutoff, graph.toarray()[aa]==1)):
if all_atoms[aa].symbol == 'H':
take_frag_idx.append(aa)
elif all_atoms[aa].symbol == 'C':
near_atom_idx = np.nonzero(np.logical_and(distancescutoff, graph.toarray()[aa]>0))[0][0]
vector = all_atoms[aa].position - all_atoms[near_atom_idx].position
new_position = all_atoms[near_atom_idx].position + vector / np.linalg.norm(vector) * 1.09
added.append(Atom('H', new_position))
elif np.count_nonzero(np.logical_and(distancescutoff, graph.toarray()[aa]>1)):
take_frag_idx=frag_atoms_idx
break
else:
take_frag_idx = frag_atoms_idx
taken_atoms_idx.append(take_frag_idx)
all_taken_atoms_idx = np.concatenate(taken_atoms_idx)
# wrap
cutoff_atoms = sum(added, all_atoms[all_taken_atoms_idx])
cutoff_atoms.wrap(
center=coords[idx] /
cutoff_atoms.get_cell_lengths_and_angles()[0: 3],
pbc=True)
coords = cutoff_atoms.get_positions()
sys.data['coords'] = np.array([coords])
sys.data['atom_types'] = np.array(list(atom_types[all_taken_atoms_idx]) + [atom_names.index('H')]*len(added))
sys.data['atom_pref'] = np.array([cutoff_atoms.get_tags()])
for ii, _ in enumerate(atom_names):
sys.data['atom_numbs'][ii] = np.count_nonzero(sys.data['atom_types']==ii)
return sys
a = Atoms('HOC', positions=[(1, 1, 1), (3, 1, 1), (6, 1, 1)])
a.set_cell((9, 2, 2))
a.set_pbc((True, False, False))
# Calculate indiviually with mic=True
assert a.get_distance(0, 1, mic=True) == 2
assert a.get_distance(1, 2, mic=True) == 3
assert a.get_distance(0, 2, mic=True) == 4
# Calculate indiviually with mic=False
assert a.get_distance(0, 1, mic=False) == 2
assert a.get_distance(1, 2, mic=False) == 3
assert a.get_distance(0, 2, mic=False) == 5
# Calculate in groups with mic=True
assert (a.get_distances(0, [1, 2], mic=True) == [2, 4]).all()
# Calculate in groups with mic=False
assert (a.get_distances(0, [1, 2], mic=False) == [2, 5]).all()
# Calculate all with mic=True
assert (a.get_all_distances(mic=True) == [[0, 2, 4],
[2, 0, 3],
[4, 3, 0]]).all()
# Calculate all with mic=False
assert (a.get_all_distances(mic=False) == [[0, 2, 5],
[2, 0, 3],
[5, 3, 0]]).all()
def take_cluster(old_conf_name, type_map, idx, jdata):
cutoff = jdata['cluster_cutoff']
cutoff_hard = jdata.get('cluster_cutoff_hard', None)
sys = dpdata.System(old_conf_name, fmt = 'lammps/dump', type_map = type_map)
atom_names = sys['atom_names']
atom_types = sys['atom_types']
cell = sys['cells'][0]
coords = sys['coords'][0]
symbols = [atom_names[atom_type] for atom_type in atom_types]
# detect fragment
frag_numb, frag_index, graph = _crd2frag(symbols, coords, True, cell, return_bonds=True)
# get_distances
all_atoms = Atoms(symbols = symbols, positions = coords, pbc=True, cell=cell)
all_atoms[idx].tag = 1
distances = all_atoms.get_distances(idx, range(len(all_atoms)), mic=True)
distancescutoff = distances < cutoff
cutoff_atoms_idx = np.where(distancescutoff)[0]
if cutoff_hard is not None:
distancescutoff_hard = distances < cutoff_hard
cutoff_atoms_idx_hard = np.where(distancescutoff_hard)[0]
# make cutoff atoms in molecules
taken_atoms_idx = []
added = []
for ii in range(frag_numb):
frag_atoms_idx = np.where(frag_index == ii)[0]
if cutoff_hard is not None:
# drop atoms out of the hard cutoff anyway
frag_atoms_idx = np.intersect1d(frag_atoms_idx, cutoff_atoms_idx_hard)
if np.any(np.isin(frag_atoms_idx, cutoff_atoms_idx)):
if 'cluster_minify' in jdata and jdata['cluster_minify']:
# support for organic species
take_frag_idx=[]
for aa in frag_atoms_idx:
if np.any(np.isin(aa, cutoff_atoms_idx)):
# atom is in the soft cutoff
# pick up anyway
take_frag_idx.append(aa)
elif np.count_nonzero(np.logical_and(distancescutoff, graph.toarray()[aa]==1)):
# atom is between the hard cutoff and the soft cutoff
# and has a single bond with the atom inside
if all_atoms[aa].symbol == 'H':
# for atom H: just add it
take_frag_idx.append(aa)
else:
# for other atoms (C, O, etc.): replace it with a ghost H atom
near_atom_idx = np.nonzero(np.logical_and(distancescutoff, graph.toarray()[aa]>0))[0][0]
vector = all_atoms[aa].position - all_atoms[near_atom_idx].position
new_position = all_atoms[near_atom_idx].position + vector / np.linalg.norm(vector) * 1.09
added.append(Atom('H', new_position))
elif np.count_nonzero(np.logical_and(distancescutoff, graph.toarray()[aa]>1)):
# if that atom has a double bond with the atom inside
# just pick up the whole fragment (within the hard cutoff)
# TODO: use a more fantastic method
take_frag_idx=frag_atoms_idx
break
else:
take_frag_idx = frag_atoms_idx
taken_atoms_idx.append(take_frag_idx)
all_taken_atoms_idx = np.concatenate(taken_atoms_idx)
# wrap
cutoff_atoms = sum(added, all_atoms[all_taken_atoms_idx])
cutoff_atoms.wrap(
center=coords[idx] /
cutoff_atoms.get_cell_lengths_and_angles()[0: 3],
pbc=True)
coords = cutoff_atoms.get_positions()
sys.data['coords'] = np.array([coords])
sys.data['atom_types'] = np.array(list(atom_types[all_taken_atoms_idx]) + [atom_names.index('H')]*len(added))
sys.data['atom_pref'] = np.array([cutoff_atoms.get_tags()])
for ii, _ in enumerate(atom_names):
sys.data['atom_numbs'][ii] = np.count_nonzero(sys.data['atom_types']==ii)
return sys
a = Atoms('HOC', positions=[(1, 1, 1), (3, 1, 1), (6, 1, 1)])
a.set_cell((9, 2, 2))
a.set_pbc((True, False, False))
# Calculate indiviually with mic=True
assert a.get_distance(0, 1, mic=True) == 2
assert a.get_distance(1, 2, mic=True) == 3
assert a.get_distance(0, 2, mic=True) == 4
# Calculate indiviually with mic=False
assert a.get_distance(0, 1, mic=False) == 2
assert a.get_distance(1, 2, mic=False) == 3
assert a.get_distance(0, 2, mic=False) == 5
# Calculate in groups with mic=True
assert (a.get_distances(0, [1, 2], mic=True) == [2, 4]).all()
# Calculate in groups with mic=False
assert (a.get_distances(0, [1, 2], mic=False) == [2, 5]).all()
# Calculate all with mic=True
assert (a.get_all_distances(mic=True) == [[0, 2, 4], [2, 0, 3], [4, 3,
0]]).all()
# Calculate all with mic=False
assert (a.get_all_distances(mic=False) == [[0, 2, 5], [2, 0, 3], [5, 3,
0]]).all()
# Scale Distance
old = a.get_distance(0, 1)
a.set_distance(0, 1, 0.9, add=True, factor=True)
def change_cell_length(atoms, space_group):
print(atoms.get_atomic_numbers())
name = get_name(atoms.get_atomic_numbers())
print(name)
# to do
molecule1, molecule2, molecule3, molecule4 = molecule_lists(
atoms)[0], molecule_lists(atoms)[1], molecule_lists(
atoms)[2], molecule_lists(atoms)[3] # [1,5,9,13,17,21,etc]
print(molecule1)
print(molecule2)
print(molecule3)
print(molecule4)
scaled_positions = atoms.get_scaled_positions()
#print("scaled_positions: ", scaled_positions)
molecule1_scaled_positions = np.array(
[scaled_positions[i] for i in molecule1])
cell_params = atoms.get_cell()
#print(cell_params)
#print(atoms.get_positions())
a_vector, b_vector, c_vector = cell_params[0], cell_params[1], cell_params[
2]
molecule1_vectors = np.array([
faction[0] * a_vector + faction[1] * b_vector + faction[2] * c_vector
for faction in molecule1_scaled_positions
])
new_atoms = atoms.copy()
new_atoms.set_cell(cell_params +
np.array([[1, 0, 0], [0, 1, 0], [0.1, 0, 1]]),
scale_atoms=False)
new_cell_params = new_atoms.get_cell()
print("new_cell_params: ", new_cell_params)
new_a_vector, new_b_vector, new_c_vector = new_cell_params[
0], new_cell_params[1], new_cell_params[2]
new_vectors = []
for v in molecule1_vectors:
Va = np.dot(
np.cross(new_b_vector, new_c_vector) /
np.dot(new_a_vector, np.cross(new_b_vector, new_c_vector)), v)
Vb = np.dot(
np.cross(new_c_vector, new_a_vector) /
np.dot(new_b_vector, np.cross(new_c_vector, new_a_vector)), v)
Vc = np.dot(
np.cross(new_a_vector, new_b_vector) /
np.dot(new_c_vector, np.cross(new_a_vector, new_b_vector)), v)
new_vectors.append([Va, Vb, Vc])
new_sclaed_positions = np.array(new_vectors)
print("get_symop(): ", space_group.get_symop())
sites = []
for kind, pos in enumerate(new_sclaed_positions):
for rot, trans in space_group.get_symop():
site = np.dot(rot, pos) + trans
sites.append(site)
print(np.array(sites))
new_positions = np.array([
faction[0] * new_a_vector + faction[1] * new_b_vector +
faction[2] * new_c_vector for faction in sites
])
print(new_positions)
#wire = Atoms('',
# positions=[[0, L / 2, L / 2]],
# cell=[d, L, L],
# pbc=[1, 0, 0])
writer = Atoms(name,
positions=new_positions,
cell=new_atoms.get_cell(),
pbc=[1, 1, 1])
#final_scaled_positions = get_equivalent_sites(new_sclaed_positions, space_group)
#print("final_scaled_positions: ", final_scaled_positions)
#new_atoms.set_scaled_positions(final_scaled_positions)
for i in molecule1:
print(
writer.get_distances(i, molecule1) -
atoms.get_distances(i, molecule1))
#print(atoms.get_distance(24,36, mic=False, vector=True))
#print(new_atoms.get_distance(24,36, mic=False, vector=True))
print(writer.get_cell())
return writer
