def draw_edge(self, i, j):
ci = self.coord[i] #0..1
cj = self.coord[j]
d = cj - ci
d -= np.floor(d + 0.5)
xi = np.dot(ci, self.cell)
xj = np.dot(ci + d, self.cell)
if self.has_edge(i, j):
return yp.Color(4) + yp.ArrowType(2) + yp.Arrow(xi, xj)
elif self.has_edge(j, i):
return yp.Color(5) + yp.ArrowType(2) + yp.Arrow(xj, xi)
else:
return yp.Color(0) + yp.Line(xi, xj)
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 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.")