def mayavi(structure, N=10):
""" import this module and run mayavi to see the divide and conquer boxes.
Enjoy and play around.
"""
from enthought.mayavi.mlab import points3d
from pylada.crystal.cppwrappers import periodic_dnc
mesh, boxes = periodic_dnc(structure, nperbox=30, overlap=0.25, return_mesh = True)
x, y, z, s = [], [], [], []
for i, box in enumerate(boxes):
if i == N: continue
x.extend([(atom.pos[0] + trans[0]) for atom, trans, inbox in box if inbox])
y.extend([(atom.pos[1] + trans[1]) for atom, trans, inbox in box if inbox])
z.extend([(atom.pos[2] + trans[2]) for atom, trans, inbox in box if inbox])
s.extend([0.5 for atom, trans, inbox in box if inbox])
points3d(x,y,z,s, scale_factor=0.1, colormap="copper")
x, y, z, s = [], [], [], []
for i, box in enumerate(boxes):
if i < N: continue
x.extend([(atom.pos[0] + trans[0]) for atom, trans, inbox in box if inbox])
y.extend([(atom.pos[1] + trans[1]) for atom, trans, inbox in box if inbox])
z.extend([(atom.pos[2] + trans[2]) for atom, trans, inbox in box if inbox])
s.extend([float(i+1) + (0. if inbox else 0.4) for atom, trans, inbox in box if inbox])
break
points3d(x,y,z,s, scale_factor=0.004, colormap="autumn")
x, y, z, s = [], [], [], []
for i, box in enumerate(boxes):
if i < N: continue
x.extend([(atom.pos[0] + trans[0]) for atom, trans, inbox in box if not inbox])
y.extend([(atom.pos[1] + trans[1]) for atom, trans, inbox in box if not inbox])
z.extend([(atom.pos[2] + trans[2]) for atom, trans, inbox in box if not inbox])
s.extend([float(i+2) + (0. if inbox else 0.4) for atom, trans, inbox in box if not inbox])
break
points3d(x,y,z,s, scale_factor=0.01, opacity=0.3)
def check(structure):
from numpy import multiply, cast, any
from numpy.linalg import inv
from pylada.crystal.cppwrappers import periodic_dnc
from pylada.math import gruber
mesh, boxes = periodic_dnc(structure, nperbox=30, overlap=0.125, return_mesh = True)
invcell = gruber(structure.cell)
invcell[:, 0] /= float(mesh[0])
invcell[:, 1] /= float(mesh[1])
invcell[:, 2] /= float(mesh[2])
invcell = inv(invcell)
for box in boxes:
assert any(u[2] for u in box)
for atom, trans, inbox in box:
if inbox: break
index = indices(invcell, trans+atom.pos, mesh)
for atom, trans, inbox in box:
pi = indices(invcell, trans+atom.pos, mesh)
if inbox: assert all(abs(pi - index) < 1e-8), (pi, index)
else:
assert any( abs(u-v) == 1 \
or (w>1 and abs(u-v) == w-1) \
or w == 1 for u, v, w in zip(pi, index, mesh) )