def print_imag_vector(self, mode_number=6, name=None):
"""Print a .xyz file with multiple structures visualising the largest
magnitude imaginary mode
Keyword Arguments:
mode_number (int): Number of the normal mode to visualise,
6 (default) is the lowest frequency vibration
i.e. largest magnitude imaginary, if present
name (str):
"""
assert self.optts_calc is not None
name = self.name if name is None else name
disp = -0.5
for i in range(40):
atoms = get_displaced_atoms_along_mode(
calc=self.optts_calc,
mode_number=int(mode_number),
disp_magnitude=disp,
atoms=self.atoms)
atoms_to_xyz_file(atoms=atoms, filename=f'{name}.xyz', append=True)
# Add displacement so the final set of atoms are +0.5 Å displaced
# along the mode, then displaced back again
sign = 1 if i < 20 else -1
disp += sign * 1.0 / 20.0
return None
def print_geometries(self, name):
"""Print an xyz trajectory of the geometries in the path"""
# Empty the file
open(f'{name}.xyz', 'w').close()
for i, image in enumerate(self):
assert image.species is not None
energy = image.energy if image.energy is not None else 'none'
atoms_to_xyz_file(image.species.atoms,
f'{name}.xyz',
title_line=f'autodE path point {i}. E = {energy}',
append=True)
return None
def print_xyz_file(self, title_line='', filename=None):
"""Print a standard xyz file from the Molecule's atoms"""
if filename is None:
filename = f'{self.name}.xyz'
return atoms_to_xyz_file(self.atoms, filename, title_line=title_line)
def test_making_xyz_file():
atoms = [Atom('H'), Atom('H')]
atoms_to_xyz_file(atoms, filename='test.xyz')
atoms_to_xyz_file(atoms, filename='test.xyz', append=False)
xyz_lines = open('test.xyz', 'r').readlines()
assert len(xyz_lines) == 4
# With append should add the next set of atoms to the same file
atoms_to_xyz_file(atoms, filename='test.xyz', append=True)
xyz_lines = open('test.xyz', 'r').readlines()
assert len(xyz_lines) == 8
with pytest.raises(AssertionError):
# Requires some atoms
atoms_to_xyz_file(atoms=None, filename='test.xyz')
# Needs .xyz extension
atoms_to_xyz_file(atoms, filename='test')
os.remove('test.xyz')
def get_simanl_atoms(species, dist_consts=None, conf_n=0, save_xyz=True):
"""
Use a bonded + repulsive force field to generate 3D structure for a
species. If the initial coordinates are reasonable e.g. from a previously
generated 3D structure then add random displacement vectors and minimise
to generate a conformer. Otherwise add atoms to the box sequentially
until all atoms have been added, which generates a qualitatively reasonable
3D geometry which should be optimised using a electronic structure method
V(x) = Σ_bonds k(d - d0)^2 + Σ_ij c/d^n
Arguments:
species (autode.species.Species):
Keyword Arguments:
dist_consts (dict): Key = tuple of atom indexes, Value = distance
conf_n (int): Number of this conformer
save_xyz (bool): Whether or not to save a .xyz file of the structure
for fast reloading
Returns:
(list(autode.atoms.Atom)): Atoms
"""
xyz_filename = f'{species.name}_conf{conf_n}_siman.xyz'
saved_atoms = get_atoms_from_generated_file(species, xyz_filename)
if saved_atoms is not None:
return saved_atoms
# To generate the potential requires bonds between atoms defined in a
# molecular graph
if species.graph is None:
raise ex.NoMolecularGraph
# Initialise a new random seed and make a copy of the species' atoms.
# RandomState is thread safe
rand = np.random.RandomState()
atoms = get_atoms_rotated_stereocentres(species=species,
atoms=deepcopy(species.atoms),
rand=rand)
# Add the distance constraints as fixed bonds
d0 = get_ideal_bond_length_matrix(atoms=species.atoms,
bonds=species.graph.edges())
# Add distance constraints across stereocentres e.g. for a Z double bond
# then modify d0 appropriately
dist_consts = add_dist_consts_for_stereocentres(
species=species,
dist_consts={} if dist_consts is None else dist_consts)
constrained_bonds = []
for bond, length in dist_consts.items():
i, j = bond
d0[i, j] = length
d0[j, i] = length
constrained_bonds.append(bond)
# Randomise coordinates that aren't fixed by shifting a maximum of
# autode.Config.max_atom_displacement in x, y, z
fixed_atom_indexes = get_non_random_atoms(species=species)
# Shift by a factor defined in the config file if the coordinates are
# reasonable but otherwise init in a 10 A cube
reasonable_init_coords = ade.geom.are_coords_reasonable(
species.coordinates)
if reasonable_init_coords:
factor = ade.Config.max_atom_displacement / np.sqrt(3)
for i, atom in enumerate(atoms):
if i not in fixed_atom_indexes:
atom.translate(vec=factor * rand.uniform(-1, 1, 3))
else:
# Randomise in a 10 Å cubic box
[atom.translate(vec=rand.uniform(-5, 5, 3)) for atom in atoms]
logger.info('Minimising species...')
st = time()
if reasonable_init_coords:
coords = get_coords_minimised_v(coords=np.array(
[atom.coord for atom in atoms]),
bonds=species.graph.edges,
k=1.0,
c=0.01,
d0=d0,
tol=1E-5,
fixed_bonds=constrained_bonds)
else:
coords = get_coords_no_init_strucutre(atoms, species, d0,
constrained_bonds)
logger.info(f' ... ({time()-st:.3f} s)')
# Set the coordinates of the new atoms
for i, atom in enumerate(atoms):
atom.coord = coords[i]
# Print an xyz file so rerunning will read the file
if save_xyz:
atoms_to_xyz_file(atoms=atoms, filename=xyz_filename)
return atoms
