def set_nsc(self, nsc=None, a=None, b=None, c=None):
""" Sets the number of supercells in the 3 different cell directions
nsc: list of int, optional
number of supercells in each direction
a: integer, optional
number of supercells in the first unit-cell vector direction
b: integer, optional
number of supercells in the second unit-cell vector direction
c: integer, optional
number of supercells in the third unit-cell vector direction
"""
if not nsc is None:
for i in range(3):
if not nsc[i] is None:
self.nsc[i] = nsc[i]
if a:
self.nsc[0] = a
if b:
self.nsc[1] = b
if c:
self.nsc[2] = c
# Correct for misplaced number of unit-cells
for i in range(3):
if self.nsc[i] == 0:
self.nsc[i] = 1
if np.sum(self.nsc % 2) != 3:
raise ValueError(
"Supercells has to be of un-even size. The primary cell counts "
+ "one, all others count 2")
# We might use this very often, hence we store it
self.n_s = _a.prodi(self.nsc)
self._sc_off = _a.zerosi([self.n_s, 3])
self._isc_off = _a.zerosi(self.nsc)
n = self.nsc
# We define the following ones like this:
def ret_range(val):
i = val // 2
return range(-i, i + 1)
x = ret_range(n[0])
y = ret_range(n[1])
z = ret_range(n[2])
i = 0
for iz in z:
for iy in y:
for ix in x:
if ix == 0 and iy == 0 and iz == 0:
continue
# Increment index
i += 1
# The offsets for the supercells in the
# sparsity pattern
self._sc_off[i, 0] = ix
self._sc_off[i, 1] = iy
self._sc_off[i, 2] = iz
self._update_isc_off()
def read_geometry(self):
""" Reading a geometry in regular Hamiltonian format """
cell = np.zeros([3, 3], np.float64)
Z = []
xyz = []
nsc = _a.zerosi([3])
def Z2no(i, no):
try:
# pure atomic number
return int(i), no
except Exception:
# both atomic number and no
j = i.replace('[', ' ').replace(']', ' ').split()
return int(j[0]), int(j[1])
# The format of the geometry file is
keys = ['atoms', 'cell', 'supercell', 'nsc']
for _ in range(len(keys)):
_, l = self.step_to(keys, case=False)
l = l.strip()
if 'supercell' in l.lower() or 'nsc' in l.lower():
# We have everything in one line
l = l.split()[1:]
for i in range(3):
nsc[i] = int(l[i])
elif 'cell' in l.lower():
if 'begin' in l.lower():
for i in range(3):
l = self.readline().split()
cell[i, 0] = float(l[0])
cell[i, 1] = float(l[1])
cell[i, 2] = float(l[2])
self.readline() # step past the block
else:
# We have everything in one line
l = l.split()[1:]
for i in range(3):
cell[i, i] = float(l[i])
# TODO incorporate rotations
elif 'atoms' in l.lower():
l = self.readline()
while not l.startswith('end'):
ls = l.split()
try:
no = int(ls[4])
except Exception:
no = 1
z, no = Z2no(ls[0], no)
Z.append({'Z': z, 'orbital': [-1. for _ in range(no)]})
xyz.append([float(f) for f in ls[1:4]])
l = self.readline()
xyz = _a.arrayd(xyz)
xyz.shape = (-1, 3)
self.readline() # step past the block
# Create geometry with associated supercell and atoms
geom = Geometry(xyz, atoms=Atom[Z], sc=SuperCell(cell, nsc))
return geom