def hook6(lattice):
global nwateratoms
lattice.logger.info("Hook6: Output water molecules in Yaplot format.")
lattice.logger.info(" Total number of atoms: {0}".format(
len(lattice.atoms)))
# prepare the reverse dict
waters = defaultdict(dict)
for atom in lattice.atoms:
resno, resname, atomname, position, order = atom
if "O" in atomname:
waters[order]["O"] = position
elif "H" in atomname:
if "H0" not in waters[order]:
waters[order]["H0"] = position
else:
waters[order]["H1"] = position
s = ""
s += yp.Color(3)
for order, water in waters.items():
O = water["O"]
H0 = water["H0"]
H1 = water["H1"]
s += yp.Layer(4)
s += yp.Color(3)
s += yp.Size(0.03)
s += yp.Circle(O)
s += yp.Line(O, H0)
s += yp.Line(O, H1)
s += yp.Size(0.01)
s += yp.Circle(H0)
s += yp.Circle(H1)
s += yp.Color(2)
s += yp.Layer(1)
s += yp.Text(O, "{0}".format(order))
s += yp.Layer(3)
s += yp.Color(4)
s += yp.ArrowType(1)
s += yp.Size(0.03)
for i, j in lattice.graph.edges(data=False):
if i in waters and j in waters: # edge may connect to the dopant
O = waters[j]["O"]
H0 = waters[i]["H0"]
H1 = waters[i]["H1"]
d0 = H0 - O
d1 = H1 - O
rr0 = np.dot(d0, d0)
rr1 = np.dot(d1, d1)
if rr0 < rr1 and rr0 < 0.27**2:
s += yp.Arrow(H0, O)
if rr1 < rr0 and rr1 < 0.245**2:
s += yp.Arrow(H1, O)
print(s, end="")
nwateratoms = len(lattice.atoms)
lattice.logger.info("Hook6: end.")
def hook7(lattice):
global nwateratoms
lattice.logger.info("Hook7: Output water molecules in Yaplot format.")
lattice.logger.info(" Total number of atoms: {0}".format(
len(lattice.atoms)))
gatoms = lattice.atoms[nwateratoms:]
palettes = dict()
s = ""
s += yp.Layer(4)
s += yp.ArrowType(1)
H = []
O = ""
for atom in gatoms:
resno, resname, atomname, position, order = atom
if atomname in palettes:
pal = palettes[atomname]
else:
pal = 4 + len(palettes)
palettes[atomname] = pal
s += yp.Color(pal)
s += yp.Size(0.04)
s += yp.Circle(position)
s = '#' + "\n#".join(lattice.doc) + "\n" + s
print(s)
lattice.logger.info("Hook7: end.")
def depolarize(spaceicegraph, cell, draw=None):
"""
Find a farthest atom (apsis) from the given atom, and
make the shortest paths between them.
It works much better than depolarize()
"""
logger = logging.getLogger()
logger.debug(" isZ4: {0}".format(spaceicegraph.isZ4()))
logger.debug(" defects: {0}".format(spaceicegraph.defects()))
spaceicegraph.vector_check()
s = "" # for yaplot
while True:
net_polar = spaceicegraph.net_polarization()
logger.info(" Net polarization: {0}".format(net_polar))
if np.dot(net_polar, net_polar) < 0.2**2:
break # without problem
if -1 <= net_polar[0] <= 1 and -1 <= net_polar[
1] <= 1 and -1 <= net_polar[2] <= 1:
logger.info(" Gave up eliminating the polarization.")
break
if net_polar[0] > 1.0:
logger.debug("Depolarize +X")
axis = np.array([+1.0, 0.0, 0.0])
elif net_polar[0] < -1.0:
logger.debug("Depolarize -X")
axis = np.array([-1.0, 0.0, 0.0])
elif net_polar[1] > 1.0:
logger.debug("Depolarize +Y")
axis = np.array([0.0, +1.0, 0.0])
elif net_polar[1] < -1.0:
logger.debug("Depolarize -Y")
axis = np.array([0.0, -1.0, 0.0])
elif net_polar[2] > 1.0:
logger.debug("Depolarize +Z")
axis = np.array([0.0, 0.0, +1.0])
elif net_polar[2] < -1.0:
logger.debug("Depolarize -Z")
axis = np.array([0.0, 0.0, -1.0])
cycle = traversing_cycle(spaceicegraph, cell, axis, draw)
if cycle is not None:
edges = [(cycle[i], cycle[i + 1]) for i in range(len(cycle) - 1)]
if len(edges) != len(set(edges)):
logger.debug("The cycle is entangled.")
else:
if draw is not None:
s += yp.Size(0.03)
s += draw.draw_cell()
s += draw.draw_path(cycle)
s += yp.NewPage()
spaceicegraph.invert_path(cycle)
spaceicegraph.vector_check()
logger.debug("isZ4: {0}".format(spaceicegraph.isZ4()))
logger.debug("defects: {0}".format(spaceicegraph.defects()))
return s
def depolarize(spaceicegraph, cell, draw=None):
"""
Find a farthest atom (apsis) from the given atom, and
make the shortest paths between them.
It works much better than depolarize()
"""
logger = logging.getLogger()
logger.debug(" isZ4: {0}".format(spaceicegraph.isZ4()))
logger.debug(" defects: {0}".format(
spaceicegraph.bernal_fowler_defects()))
spaceicegraph.vector_check()
s = "" # for yaplot
# TSL
# defect-defect chains
defects = []
for node in spaceicegraph.nodes():
if spaceicegraph.degree(node) != 4:
assert spaceicegraph.degree(node) < 4
defects.append(node)
logger.info(" Non Z4: {0}".format(defects))
if len(defects) > 0:
reject_count = 10
while reject_count > 0:
net_polar = spaceicegraph.net_polarization()
# logger.info(" Net polarization: {0}".format(net_polar))
if np.dot(net_polar, net_polar) < 0.05**2:
break # without problem
while True:
orig = defects[random.randint(0, len(defects) - 1)]
if spaceicegraph.out_degree(orig) == 2:
break
while True:
dest = defects[random.randint(0, len(defects) - 1)]
if spaceicegraph.in_degree(dest) == 2:
break
path = shortest_path(spaceicegraph, orig, [
dest,
])
if path is None:
continue
logger.debug(" Dipole moment = {0}".format(
spaceicegraph.dipole_moment(path)))
new_net_polar = net_polar - spaceicegraph.dipole_moment(path) * 2
if np.linalg.norm(new_net_polar) < np.linalg.norm(net_polar):
if draw is not None:
s += yp.Size(0.03)
s += draw.draw_cell()
s += draw.draw_path(path)
s += yp.NewPage()
spaceicegraph.invert_path(path)
## chk_net_polar = spaceicegraph.net_polarization()
net_polar = new_net_polar
logger.info(" Net polarization: {0}".format(net_polar))
## assert np.linalg.norm(new_net_polar - chk_net_polar) < 1e-5
## logger.debug("New dipole {0}".format(new_net_polar))
## logger.debug("Chk dipole {0}".format(chk_net_polar))
reject_count = 10
else:
logger.debug(" Reject inversion")
reject_count -= 1
while True:
net_polar = spaceicegraph.net_polarization()
logger.info(" Net polarization: {0}".format(net_polar))
if np.dot(net_polar, net_polar) < 0.2**2:
break # without problem
if -1 <= net_polar[0] <= 1 and -1 <= net_polar[
1] <= 1 and -1 <= net_polar[2] <= 1:
logger.info(" Gave up eliminating the polarization. (2)")
break
if net_polar[0] > 1.0:
logger.debug("Depolarize +X")
axis = np.array([+1.0, 0.0, 0.0])
elif net_polar[0] < -1.0:
logger.debug("Depolarize -X")
axis = np.array([-1.0, 0.0, 0.0])
elif net_polar[1] > 1.0:
logger.debug("Depolarize +Y")
axis = np.array([0.0, +1.0, 0.0])
elif net_polar[1] < -1.0:
logger.debug("Depolarize -Y")
axis = np.array([0.0, -1.0, 0.0])
elif net_polar[2] > 1.0:
logger.debug("Depolarize +Z")
axis = np.array([0.0, 0.0, +1.0])
elif net_polar[2] < -1.0:
logger.debug("Depolarize -Z")
axis = np.array([0.0, 0.0, -1.0])
cycle = traversing_cycle(spaceicegraph, cell, axis, draw)
if cycle is not None:
edges = [(cycle[i], cycle[i + 1]) for i in range(len(cycle) - 1)]
if len(edges) != len(set(edges)):
logger.debug("The cycle is entangled.")
else:
if draw is not None:
s += yp.Size(0.03)
s += draw.draw_cell()
s += draw.draw_path(cycle)
s += yp.NewPage()
spaceicegraph.invert_path(cycle)
spaceicegraph.vector_check()
logger.debug("isZ4: {0}".format(spaceicegraph.isZ4()))
logger.debug("defects: {0}".format(spaceicegraph.bernal_fowler_defects()))
return s
