def __init__(self, atoms, vectors, cryst_mat, symops, assym_n):
self.vectors = vectors
self.cryst_mat = cryst_mat
self.symops = symops
self.assym_n = assym_n
self.atoms = atoms
self.coord_param_mat = None
self.vector_param_mat = None
self.cell = self.shift([0, 0, 0])
if self.vectors:
self.bordered_cell = [a.real_atom() for a in self.shift([0, 0, 0])]
start = Vector(0, 0, 0)
for i in range(2):
for j in range(2):
for k in range(2):
self.bordered_cell.append(
AtomVector(
'x', start + self.vectors[0] * i +
self.vectors[1] * j + self.vectors[2] * k, {}))
if self.vectors:
self.supercell = self.extended_cell(1)
else:
self.supercell = self.cell
self.neighbours = NeighbourCache(self)
def cartesian_atom(self, atom, cryst_cell=False):
vector_basis = np.array([v._data for v in self.vectors])
if (cryst_cell):
crysmat = np.array(self.cryst_mat)
vector_basis = np.transpose(crysmat).dot(vector_basis)
unrel = np.transpose(vector_basis).dot(atom.position()._data)
return AtomVector(atom.name(), Vector(unrel), {})
def reflect(c, ax1, ax2):
ax_refl = ax1.position().cross(ax2.position())
res = []
for a in c:
res.append(
AtomVector(a._name, a._vector - a._vector.projection(ax_refl) * 2))
return res
def rotate_to_axis(ax1, ax2, c2):
ax_rot = ax1.position().cross(ax2.position())
if rough_equal(ax_rot.length, 0, 0.000001):
if rough_equal(ax1.distance(ax2), 0, 0.000001):
return c2
else:
res = []
for a in c2:
res.append(AtomVector(a._name, -a._vector))
return res
angle = ax2.position().signed_angle_to(ax1.position(), ax_rot)
rot = Orientation.new_axis_angle(ax_rot, angle)
res = []
for a in c2:
res.append(AtomVector(a._name, rot * a._vector))
return res
def true_relative_atom(self, atom, cryst_cell=False):
vector_basis = np.array([v._data for v in self.vectors])
if (cryst_cell):
crysmat = np.array(self.cryst_mat)
vector_basis = np.transpose(crysmat).dot(vector_basis)
rel = np.linalg.inv(np.transpose(vector_basis)).dot(
atom.position()._data)
return AtomVector(atom.name(), Vector(rel), {})
def rotate_along(ax2, ay1, ay2, c2):
ax_rot = ax2.position()
r1 = ay1.position() - ay1.position().projection(ax_rot)
r2 = ay2.position() - ay2.position().projection(ax_rot)
angle = r2.signed_angle_to(r1, ax_rot)
rot = Orientation.new_axis_angle(ax_rot, angle)
res = []
for a in c2:
res.append(AtomVector(a._name, rot * a._vector))
return res
def real_atom(self):
return AtomVector(self.name(), self.position(), self.data())
def apply_symop(self, atom, symop):
n, inv, rot_mat, translator = symop
new_vec = np.array(rot_mat).dot(atom.position()._data)
new_vec += np.array(translator)
new_vec = self.validate_rel(new_vec)
return AtomVector(atom.name(), Vector(new_vec), {})