def test_mask_species_blacklist(self):
mask_center_atoms_by_species(self.frame, species_blacklist=["C", "H"])
test_mask = np.array([1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0], dtype="bool")
self.check_mask(test_mask)
mask_center_atoms_by_species(self.frame, species_blacklist=["N"])
test_mask[[0, 2, 4, 6]] = False
self.check_mask(test_mask)
mask_center_atoms_by_species(self.frame, species_select=["H"])
test_mask[[9, 10]] = True
self.check_mask(test_mask)
def test_mask_species_blacklist(self):
mask_center_atoms_by_species(self.frame, species_blacklist=['C', 'H'])
test_mask = np.array([1, 0, 1, 0, 1, 1, 1, 1, 1, 0, 0], dtype='bool')
self.check_mask(test_mask)
mask_center_atoms_by_species(self.frame, species_blacklist=['N'])
test_mask[[0, 2, 4, 6]] = False
self.check_mask(test_mask)
mask_center_atoms_by_species(self.frame, species_select=['H'])
test_mask[[9, 10]] = True
self.check_mask(test_mask)
def test_mask_species_numeric_combined(self):
mask_center_atoms_by_species(self.frame,
species_select=["C", "N"],
species_blacklist=[7, 1])
test_mask = np.array([0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0], dtype="bool")
self.check_mask(test_mask)
# And check that mixed symbol-numeric lists are disallowed
with self.assertRaises(ValueError):
mask_center_atoms_by_species(self.frame, species_select=["C", 1])
with self.assertRaises(ValueError):
mask_center_atoms_by_species(self.frame,
species_blacklist=["C", 1])
import numpy as np
from rascal.representations import SphericalInvariants
from rascal.neighbourlist.structure_manager import (
mask_center_atoms_by_species, mask_center_atoms_by_id)
molecules = ase.io.read('data/small_molecules-1000.xyz', ':100')
n_centers = sum(mol.get_number_of_atoms() for mol in molecules)
n_carbon_centers = sum(
np.sum(mol.get_atomic_numbers() == 6) for mol in molecules)
print("{:d} molecules, {:d} centres total, {:d} carbon centres".format(
len(molecules), n_centers, n_carbon_centers))
for molecule in molecules:
mask_center_atoms_by_species(molecule, species_select=[
'C',
])
# Also works by atomic number
#mask_center_atoms_by_species(molecule, species_select=[6,])
hypers = {
'interaction_cutoff': 5.0,
'cutoff_smooth_width': 0.5,
'max_radial': 8,
'max_angular': 6,
'gaussian_sigma_type': "Constant",
'gaussian_sigma_constant': 0.3
}
representation = SphericalInvariants(**hypers)
atoms_transformed = representation.transform(molecules)
def test_mask_species_and_id(self):
mask_center_atoms_by_species(self.frame, species_select=["C"])
mask_center_atoms_by_id(self.frame, id_blacklist=np.arange(3))
test_mask = np.zeros((self.natoms, ), dtype="bool")
test_mask[3] = True
self.check_mask(test_mask)
def test_mask_species_numeric(self):
# Can also select by atomic number
mask_center_atoms_by_species(self.frame, species_select=[1, 6])
test_mask = np.array([0, 1, 0, 1, 0, 0, 0, 0, 0, 1, 1], dtype="bool")
self.check_mask(test_mask)
def test_mask_species_both(self):
mask_center_atoms_by_species(self.frame,
species_select=["C", "N"],
species_blacklist=["N", "H"])
test_mask = np.array([0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0], dtype="bool")
self.check_mask(test_mask)
def test_mask_species_both(self):
mask_center_atoms_by_species(self.frame,
species_select=['C', 'N'],
species_blacklist=['N', 'H'])
test_mask = np.array([0, 1, 0, 1, 0, 0, 0, 0, 0, 0, 0], dtype='bool')
self.check_mask(test_mask)
mask_center_atoms_by_species,
mask_center_atoms_by_id,
)
molecules = ase.io.read("../reference_data/inputs/small_molecules-1000.xyz",
":100")
n_centers = sum(mol.get_number_of_atoms() for mol in molecules)
n_carbon_centers = sum(
np.sum(mol.get_atomic_numbers() == 6) for mol in molecules)
print("{:d} molecules, {:d} centres total, {:d} carbon centres".format(
len(molecules), n_centers, n_carbon_centers))
for molecule in molecules:
mask_center_atoms_by_species(
molecule,
species_select=[
"C",
],
)
# Also works by atomic number
# mask_center_atoms_by_species(molecule, species_select=[6,])
hypers = {
"interaction_cutoff": 5.0,
"cutoff_smooth_width": 0.5,
"max_radial": 8,
"max_angular": 6,
"gaussian_sigma_type": "Constant",
"gaussian_sigma_constant": 0.3,
}
representation = SphericalInvariants(**hypers)
